Re: [Freesurfer] how to load flat surface in freeview
External Email - Use Caution Hi, it loads the left inflated surface correctly. Il giorno mer 16 mar 2022 alle ore 23:25 Douglas N. Greve < dgr...@mgh.harvard.edu> ha scritto: > What happens if you run > freeview -f > /home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated > > > On 3/10/2022 7:32 AM, Francesca Strappini wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > I'm trying to load the flat surface that I created with this command line: > > mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d > > I tried loading the patch inside freeview but I got this error message: > [francesca@GIOVE surf]$ tksurferfv sub01_mprage lh inflated > freeview -f > /home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated:curvature=/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.curv > -viewport 3d > ASSERTION FAILED: > /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 > mris->dist_nsize == 0 > ASSERTION FAILED: > /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 > mris->dist_nsize == 0 > Errore di accesso al segmento di memoria (creato file core) > > And I tried to run this command line but nothing happened: > [francesca@GIOVE surf]$freeview -f lh.inflated:patch=lh.full.flat.patch.3d > > Thank you, > Francesca > > > > -- > Francesca Strappini, Ph.D. > Psychology Department > Sapienza University of Rome > Via dei Marsi 78, Rome 00185 Italy > Tel.: +39 392 151 4029 > E-mail: francesca.strapp...@uniroma1.it > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/13FIfs6SsaNfxivIfHt5dzrauGEJL0F0WpGh9NI2HEYdv-aSJHwdfTKKsane7ZS7_6cDuw8755anwFn2xaltSYYfph3vc470xsM8AEJor63U7SqBfrd6D4kQIZHMcPp4d2748MfFMkYJKAX9YTDVlqjLkMsfiwFIpanU_WirKt4EMfzNTTbwnj9sgdgXbof4yCOaIp7ntLQceG0EHicPMtZqFzhwQYqpvnkyM5ZfgjwRgFFK0h14JKJQPK1Loz41uDydOPV4FehAyk_i7qvKG7UJzYUmDP_DNiVuGW3Lka6vFavCf8p-57W8Kq82tgfbhZSlxy6Qd9ylGJHcfFENtsg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1rEo_bp_BrY651FGcgVYsuI9kz3hkqy1dzFBz_MSL8rRw0FlwGXE2jZF11frsXz8elP5BFfO_hKCyc2rIJx5V1SZFsL_0Scto8Euht7ITOMkGYm9iy5WeA9WqdBa_TOK0GRb99_5ZzBmrBOeWBTff2Jh7E9zw4drFNy2GyKosKmRD0E0fOiuTLbazRJvcM4C9fdRAP0jiNgeeRUCPMt9ASlI0D3Vbdo1-0l0wTjsSA7eI2VijkR3eUEtAJKElhLDPS0aDWmjXInC_D2fOFSl8byZa_a_dpS7NlZAYoG2vBvTqD0oxdF_q-KvWocRQTZaK8fNuEfLlJ5Yu_dZgCrX5GQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1rEo_bp_BrY651FGcgVYsuI9kz3hkqy1dzFBz_MSL8rRw0FlwGXE2jZF11frsXz8elP5BFfO_hKCyc2rIJx5V1SZFsL_0Scto8Euht7ITOMkGYm9iy5WeA9WqdBa_TOK0GRb99_5ZzBmrBOeWBTff2Jh7E9zw4drFNy2GyKosKmRD0E0fOiuTLbazRJvcM4C9fdRAP0jiNgeeRUCPMt9ASlI0D3Vbdo1-0l0wTjsSA7eI2VijkR3eUEtAJKElhLDPS0aDWmjXInC_D2fOFSl8byZa_a_dpS7NlZAYoG2vBvTqD0oxdF_q-KvWocRQTZaK8fNuEfLlJ5Yu_dZgCrX5GQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strapp...@uniroma1.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] how to load flat surface in freeview
External Email - Use Caution Dear Freesurfer experts, I'm trying to load the flat surface that I created with this command line: mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I tried loading the patch inside freeview but I got this error message: [francesca@GIOVE surf]$ tksurferfv sub01_mprage lh inflated freeview -f /home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated:curvature=/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.curv -viewport 3d ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0 ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0 Errore di accesso al segmento di memoria (creato file core) And I tried to run this command line but nothing happened: [francesca@GIOVE surf]$freeview -f lh.inflated:patch=lh.full.flat.patch.3d Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strapp...@uniroma1.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Cutting the Full Surface
External Email - Use Caution
Thank you!
On Wed, Mar 9, 2022, 19:28 Douglas N. Greve wrote:
> In FreeView
> Click on the brain with scissors icon ("Cut"), select your points, then
> "Cut Closed Line",
>make sure the cusror is in the patch, then hit "Fill Uncut Area", then
> save as a patch
>
>
> On 3/7/2022 12:03 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Dear FreeSurfer experts,
>
> I'm trying to cut and flatten the full surface. I understand that tksurfer
> is deprecated and on my PC does not work properly. Is there an alternative
> way to perform the cuts?
>
> Thank you,
> Francesca
>
>
>
> --
> Francesca Strappini, Ph.D.
> Psychology Department
> Sapienza University of Rome
> Via dei Marsi 78, Rome 00185 Italy
> Tel.: +39 392 151 4029
> E-mail: francesca.strapp...@uniroma1.it
>
>
> ___
> Freesurfer mailing
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>
>
> ___
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[Freesurfer] Cutting the Full Surface
External Email - Use Caution Dear FreeSurfer experts, I'm trying to cut and flatten the full surface. I understand that tksurfer is deprecated and on my PC does not work properly. Is there an alternative way to perform the cuts? Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strapp...@uniroma1.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] monkey atlas resampling
External Email - Use Caution Dear FreeSurfer experts, I'm trying to resample an anatomical monkey atlas D99 to the functional space. I run this command line: mri_vol2vol --reg registerNMT2toCassis.dat --mov D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --targ /usr/local/freesurfer/fsfast/ Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --o D99_registered2func.nii.gz However, the registration was completely lost and I had to register it again manually. Maybe I did something wrong? Thanks. Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] monkey atlas D99 {Disarmed}
External Email - Use Caution
Ok thanks. I need to extract the mean signal from the regions contained in
this nifti file. I suppose I need first to resample it in functional space
and then use mri_segstats, but I'm not sure which is the right way to do
it. Any suggestion?
On Wed, Dec 23, 2020, 19:05 Greve, Douglas N.,Ph.D.
wrote:
> The argument to the --label flag should be a freesurfer label file, this
> is a text file not an nii.gz file.
>
> On 12/21/2020 10:52 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Thank you!
> I run mri_label2vol but I got this error.
>
> mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
> --reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject
> MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
> Number of labels: 1
> D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
> Annot File: (null)
> Template Volume:
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
> Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
> Registration File: registerNMT2toCassis.dat
> Fill Threshold: 0.3
> Label Vox Vol: 1
> ProjType: frac
> ProjTypeId: 2
> ProjStart: 0
> ProjStop: 1
> ProjDelta: 0.1
> Subject: MonkeyCassis
> Hemi: lh
> UseNewASeg2Vol: 0
> DoLabelStatVol 0
> LabelCodeOffset 0
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
> $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
> Template RAS-to-Vox:
> -0.49612 -0.0 -0.0 32.0;
> -0.0 -0.0 -0.49612 32.0;
> -0.0 0.5 -0.0 10.0;
> -0.0 -0.0 -0.0 1.0;
> Template Voxel Volume: 8.12549
> nHits Thresh: 2.43765
> Loading registration from registerNMT2toCassis.dat
> RegMat:
> -0.99904 -0.03839 0.02093 -1.00375;
> 0.02331 -0.06274 0.99776 -29.26276;
> 0.03699 -0.99729 -0.06358 -8.60775;
> 0.0 0.0 0.0 1.0;
> Label RAS-to-Vox:
> 0.49565 0.01905 -0.01038 32.49799;
> -0.01835 0.49478 0.03154 36.27051;
> 0.01166 -0.03137 0.49888 -4.63138;
> 0.0 0.0 0.0 1.0;
> INFO: loading surface
> /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white
> nvertices = 16975
> Reading thickness
> /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness
> nlabels = 1
> Allocating Hit Volume (81920) voxels
> Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
>
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> �^2��ܱ��=�u���8wo�C}�[ {���M&� =<G[�X�3]�㜙췪�|��tI掝�L��
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> �y�Wu��v�iݯ��x���d��a�'s�03���C��� �=ȣ�xϲ�� ��d5�;���Nf<Ձ���3
>
>
> �s��9� �A�d��A��e��A/�;:���Lr0�y��<��d�s�QѪ���^�Oû]��
> mri_label2vol: could not scan # of lines from label file
> ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
>
> Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> ha scritto:
>
>> Use mri_label2vol to map the segmentation into the fMRI space, then use
>> mri_segstats using the --avgwf option to get time courses. Run it with
>> --help to get examples
>>
>> On 11/26/2020 9:16 AM, Francesca Strappini wrote:
>>
>> External Email - Use Caution
>> Dear FreeSurfer experts,
>>
>> I'm trying to use the monkey atlas D99. First, I registered the
>> segmentation atlas to the monkey anatomy through bbregister. Now, I need to
>> resample the segmentation to the functional data and extract the mean value
>> from each functional run using the ROIs contained in the segmentation as
>> masks. I suppose I should mri_segstats but I'm not sure how. Any
>> suggestion?
>>
>> Thank you
>> Francesca
>>
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has
>> detected a possible fraud attempt from "secure-web.cisco.com
Re: [Freesurfer] monkey atlas D99 {Disarmed}
External Email - Use Caution
Thank you!
I run mri_label2vol but I got this error.
mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
--reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject
MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
Number of labels: 1
D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Annot File: (null)
Template Volume:
/usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
Registration File: registerNMT2toCassis.dat
Fill Threshold: 0.3
Label Vox Vol: 1
ProjType: frac
ProjTypeId: 2
ProjStart: 0
ProjStop: 1
ProjDelta: 0.1
Subject: MonkeyCassis
Hemi: lh
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox:
-0.49612 -0.0 -0.0 32.0;
-0.0 -0.0 -0.49612 32.0;
-0.0 0.5 -0.0 10.0;
-0.0 -0.0 -0.0 1.0;
Template Voxel Volume: 8.12549
nHits Thresh: 2.43765
Loading registration from registerNMT2toCassis.dat
RegMat:
-0.99904 -0.03839 0.02093 -1.00375;
0.02331 -0.06274 0.99776 -29.26276;
0.03699 -0.99729 -0.06358 -8.60775;
0.0 0.0 0.0 1.0;
Label RAS-to-Vox:
0.49565 0.01905 -0.01038 32.49799;
-0.01835 0.49478 0.03154 36.27051;
0.01166 -0.03137 0.49888 -4.63138;
0.0 0.0 0.0 1.0;
INFO: loading surface
/usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white
nvertices = 16975
Reading thickness
/usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness
nlabels = 1
Allocating Hit Volume (81920) voxels
Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
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mri_label2vol: could not scan # of lines from label file
ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:
> Use mri_label2vol to map the segmentation into the fMRI space, then use
> mri_segstats using the --avgwf option to get time courses. Run it with
> --help to get examples
>
> On 11/26/2020 9:16 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Dear FreeSurfer experts,
>
> I'm trying to use the monkey atlas D99. First, I registered the
> segmentation atlas to the monkey anatomy through bbregister. Now, I need to
> resample the segmentation to the functional data and extract the mean value
> from each functional run using the ROIs contained in the segmentation as
> masks. I suppose I should mri_segstats but I'm not sure how. Any
> suggestion?
>
> Thank you
> Francesca
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il
>
> ___
> Freesurfer mailing
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>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1OSQzH25ch8h2koY-2WgW3vl2N5u_7AcNIyzIWDo69jLql0pA2DXIIaahni8EcIy68SNACHeoWD7dNzPDAR1J0vFU-LJTNAWTU38-LHnMIuz3DAt-DvC5T9XdBs_xRmsniCTrNd6q69Mb1bHR4VqRYgspTedJxTSI2dHHcAA4YFZF-7gwZHLBsd1cPxnBy281dCCtn2Xa-K3-4DhAL_FDGdAKRRcx6qutksc9N8xS8uMDBOqN0b37yC3-Fi3QwlK7M2Z3A-6AT9tdzZ-RfXEQ9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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[Freesurfer] monkey atlas D99
External Email - Use Caution Dear FreeSurfer experts, I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion? Thank you Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] license error
n.html -- -- Error ConvertSurface (SUMA_ConvertSurface.c:589): if_name lh.pial.asc not found. failure: could not create surface lh.pial.gii --> is your FreeSurfer license installed? program failure: exiting... Thanks for the help Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mkanalysis-sess with a customized HRF
External Email - Use Caution Dear Freesurfer's experts, I would like to use a customized HRF with mkanalysis-sess. Is there a way to do it? Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Hi Doug, Sorry to bother, maybe my last message got lost. Do you think you can advice me on this type of registration? Thanks! Best Francesca On Fri, Feb 22, 2019, 11:44 PM Francesca Strappini < francescastrapp...@gmail.com> wrote: > What is the best procedure? I really have no idea, I've been tried so many > things but nothing worked... > > Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> ha scritto: > >> You will need to either get the ROIs into the anatomical space or compute >> a new registration to the space of the ROIs from the functional template >> >> On 2/22/19 3:43 PM, Francesca Strappini wrote: >> >> External Email - Use Caution >> Thanks! >> The vox2ras matrices are not same. >> >> This is one region: >> >> francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info >> sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz >> Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz >> type: nii >> dimensions: 64 x 64 x 50 >>voxel sizes: 3.00, 3.00, 3.00 >> type: FLOAT (3) >>fov: 192.000 >>dof: 0 >> xstart: -96.0, xend: 96.0 >> ystart: -96.0, yend: 96.0 >> zstart: -75.0, zend: 75.0 >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 >> degrees >>nframes: 1 >>PhEncDir: UNKNOWN >>FieldStrength: 0.00 >> ras xform present >> xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = >> -2.2923 >> : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = >> 19.4768 >> : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = >> 25.1269 >> Orientation : LAS >> Primary Slice Direction: axial >> >> voxel to ras transform: >>-2.9964 0.0704 0.128188.1380 >> 0.0373 2.9106 -0.7261 -56.7017 >> 0.1414 0.7237 2.9080 -75.2534 >> 0. 0. 0. 1. >> >> voxel-to-ras determinant -27 >> >> ras to voxel transform: >>-0.3329 0.0041 0.015730.7614 >> 0.0078 0.3234 0.080423.6988 >> 0.0142 -0.0807 0.323118.4853 >>-0. -0. -0. 1. >> >> Orig: >> >> francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info >> orig.mgz >> Volume information for orig.mgz >> type: MGH >> dimensions: 256 x 256 x 256 >>voxel sizes: 1.00, 1.00, 1.00 >> type: UCHAR (0) >>fov: 256.000 >>dof: 0 >> xstart: -128.0, xend: 128.0 >> ystart: -128.0, yend: 128.0 >> zstart: -128.0, zend: 128.0 >> TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: >> 0.00 degrees >>nframes: 1 >>PhEncDir: UNKNOWN >>FieldStrength: 0.00 >> ras xform present >> xform info: x_r = -1., y_r = 0., z_r = 0., c_r = >> -2.3092 >> : x_a = 0., y_a = 0., z_a = 1., c_a = >> 26.4827 >> : x_s = 0., y_s = -1., z_s = 0., c_s = >> 19.0338 >> >> talairach xfm : >> /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm >> Orientation : LIA >> Primary Slice Direction: coronal >> >> voxel to ras transform: >>-1. 0. 0. 125.6908 >> 0. 0. 1. -101.5173 >> 0. -1. 0. 147.0338 >> 0. 0. 0. 1. >> >> voxel-to-ras determinant -1 >> >> ras to voxel transform: >>-1. 0. 0. 125.6908 >>-0. 0. -1. 147.0338 >>-0. 1. 0. 101.5173 >>-0. -0. -0. 1. >> >> This is the raw T1 to which the regions are registered: >> >> Volume information for >> sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz >> type: nii >> dimensions: 256 x 256 x 192 >>voxel sizes: 1.00, 1.00, 1.00 >> type: FLOAT (3) >>fov: 256.000 >>dof: 0 >> xstart: -128.0, xend: 128.0 >> ystart: -128.0, yend:
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution What is the best procedure? I really have no idea, I've been tried so many things but nothing worked... Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > You will need to either get the ROIs into the anatomical space or compute > a new registration to the space of the ROIs from the functional template > > On 2/22/19 3:43 PM, Francesca Strappini wrote: > > External Email - Use Caution > Thanks! > The vox2ras matrices are not same. > > This is one region: > > francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info > sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz > Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz > type: nii > dimensions: 64 x 64 x 50 >voxel sizes: 3.00, 3.00, 3.00 > type: FLOAT (3) >fov: 192.000 >dof: 0 > xstart: -96.0, xend: 96.0 > ystart: -96.0, yend: 96.0 > zstart: -75.0, zend: 75.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees >nframes: 1 >PhEncDir: UNKNOWN >FieldStrength: 0.00 > ras xform present > xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = > -2.2923 > : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = > 19.4768 > : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = > 25.1269 > Orientation : LAS > Primary Slice Direction: axial > > voxel to ras transform: >-2.9964 0.0704 0.128188.1380 > 0.0373 2.9106 -0.7261 -56.7017 > 0.1414 0.7237 2.9080 -75.2534 > 0. 0. 0. 1. > > voxel-to-ras determinant -27 > > ras to voxel transform: >-0.3329 0.0041 0.015730.7614 > 0.0078 0.3234 0.080423.6988 > 0.0142 -0.0807 0.323118.4853 >-0. -0. -0. 1. > > Orig: > > francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info > orig.mgz > Volume information for orig.mgz > type: MGH > dimensions: 256 x 256 x 256 >voxel sizes: 1.00, 1.00, 1.00 > type: UCHAR (0) >fov: 256.000 >dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: > 0.00 degrees >nframes: 1 >PhEncDir: UNKNOWN >FieldStrength: 0.00 > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > -2.3092 > : x_a = 0., y_a = 0., z_a = 1., c_a = > 26.4827 > : x_s = 0., y_s = -1., z_s = 0., c_s = > 19.0338 > > talairach xfm : > /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: >-1. 0. 0. 125.6908 > 0. 0. 1. -101.5173 > 0. -1. 0. 147.0338 > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: >-1. 0. 0. 125.6908 >-0. 0. -1. 147.0338 >-0. 1. 0. 101.5173 >-0. -0. -0. 1. > > This is the raw T1 to which the regions are registered: > > Volume information for > sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz > type: nii > dimensions: 256 x 256 x 192 >voxel sizes: 1.00, 1.00, 1.00 > type: FLOAT (3) >fov: 256.000 >dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -96.0, zend: 96.0 > TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: > 0.00 degrees >nframes: 1 >PhEncDir: UNKNOWN >FieldStrength: 0.00 > ras xform present > xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = > -2.3092 > : x_a = -0.9823, y_a = 0.1874, z_a = -0., c_a = > 26.4827 > : x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = > 19.0338 > Orientation : PIL > Primary Slice Direction: sagittal > > voxel to ras transform: >-0.0069 -0.0360 -0.999399.1125 >-0.9823 0.1874
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Thanks! The vox2ras matrices are not same. This is one region: francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz type: nii dimensions: 64 x 64 x 50 voxel sizes: 3.00, 3.00, 3.00 type: FLOAT (3) fov: 192.000 dof: 0 xstart: -96.0, xend: 96.0 ystart: -96.0, yend: 96.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.00 ras xform present xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = -2.2923 : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = 19.4768 : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = 25.1269 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.9964 0.0704 0.128188.1380 0.0373 2.9106 -0.7261 -56.7017 0.1414 0.7237 2.9080 -75.2534 0. 0. 0. 1. voxel-to-ras determinant -27 ras to voxel transform: -0.3329 0.0041 0.015730.7614 0.0078 0.3234 0.080423.6988 0.0142 -0.0807 0.323118.4853 -0. -0. -0. 1. Orig: francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.00, 1.00, 1.00 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -2.3092 : x_a = 0., y_a = 0., z_a = 1., c_a = 26.4827 : x_s = 0., y_s = -1., z_s = 0., c_s = 19.0338 talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 125.6908 0. 0. 1. -101.5173 0. -1. 0. 147.0338 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 125.6908 -0. 0. -1. 147.0338 -0. 1. 0. 101.5173 -0. -0. -0. 1. This is the raw T1 to which the regions are registered: Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz type: nii dimensions: 256 x 256 x 192 voxel sizes: 1.00, 1.00, 1.00 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -96.0, zend: 96.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.00 ras xform present xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = -2.3092 : x_a = -0.9823, y_a = 0.1874, z_a = -0., c_a = 26.4827 : x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = 19.0338 Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0069 -0.0360 -0.999399.1125 -0.9823 0.1874 -0. 128.2306 -0.1873 -0.9816 0.0366 165.1330 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -0.0069 -0.9823 -0.1873 157.5619 -0.0360 0.1874 -0.9816 141.6386 -0.9993 0. 0.036692.9949 -0. -0. -0. 1. Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > That looks right. Can you verify that the seg (sourcedata...) is in the > conformed anatomical space? Use mri_info can compare the output > (particularly the vox2ras matrix) against orig.mgz. If they are the same, > you can try adding --invertmtx to the mri_label2vol command line. > > On 2/22/19 2:24 PM, Francesca Strappini wrote: > > External Email - Use Caution > Thanks a lot, Doug! > I run the preprocessing: > preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session > And the runs look well registered. > >
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Thanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered. Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1. Best Francesca Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > There should be a registration file called register.dof6.lta. Use that > with mri_label2vol passing your segmentation in with --seg. Run with --help > to get more info > > On 2/21/19 11:54 AM, Francesca Strappini wrote: > > External Email - Use Caution > Thanks a lot! > Running preproc-sess with the --per-session flag is exactly was I was > looking for! > Now that my functional runs are correctly registered to a reference image > (so, to each other) I need to register them to a dataset of ROIs that were > created outside freesurfer. These regions are in volume space and have the > same resolution and box size of the functional runs. They are registered to > the T1 that was used for the reconstruction of the surface. I've tried > different functions for the registration but nothing really worked. I > suppose I need a registration matrix that relates these regions to the > reference image I used during the preprocessing and to apply this to each > region. What's the best procedure? > > Best > Francesca > > > Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> ha scritto: > >> Yes, if you run it with the --targ as orig.mgz for the given subject, >> then it will sample each run into the anatomical space (this can create >> enourmous data data files!). Alternatively, you can run preproc-sess >> with the --per-session flag and it will align all the runs to a single >> template but otherwise keep everything in the functional space >> >> On 2/20/19 11:53 AM, Francesca Strappini wrote: >> > >> > External Email - Use Caution >> > >> > I'll try to find some visual way to show what I mean, but it's really >> > something mild and probably negligible. >> > Do you know if is it possible with mri_vol2vol to give to all the runs >> > that belong to the same subject the same system coordinates? So that >> > each voxel across runs will have the same coordinates. I noticed that >> > the transformation matrix is written in the header but it's not really >> > applied to the data. Thank you! >> > >> > >> > Best >> > Francesca >> > >> > >> > On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl >> > mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> > >> > Hi Francesca >> > >> > can you send us an image that shows why you think it can be >> improved? >> > >> > cheers >> > Bruce >> > On >> > Mon, 18 Feb 2019, Francesca Strappini wrote: >> > >> > > >> > > External Email - Use Caution >> > > >> > > Thank you!Now the registration is better but still not perfect. >> > Is there a way to improve it? >> > > >> > > Best >> > > >> > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. >> > mailto:dgr...@mgh.harvard.edu>> ha >> > > scritto: >> > > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 >> > weighted? If so, >> > > you should use --t2 instead of --t1 in bbregister >> > > >> > > On 2/14/19 2:18 PM, Francesca Strappini wrote: >> > > > >> > > > External Email - Use Caution >> > > > >> > > > Hi Doug, >> > > > >> > > > Could you advise me about how to correctly run >> mri_vol2vol? >> > > > The functional data did not get perfectly registered to >> > the anatomy so >> > > >
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure? Best Francesca Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > Yes, if you run it with the --targ as orig.mgz for the given subject, > then it will sample each run into the anatomical space (this can create > enourmous data data files!). Alternatively, you can run preproc-sess > with the --per-session flag and it will align all the runs to a single > template but otherwise keep everything in the functional space > > On 2/20/19 11:53 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > I'll try to find some visual way to show what I mean, but it's really > > something mild and probably negligible. > > Do you know if is it possible with mri_vol2vol to give to all the runs > > that belong to the same subject the same system coordinates? So that > > each voxel across runs will have the same coordinates. I noticed that > > the transformation matrix is written in the header but it's not really > > applied to the data. Thank you! > > > > > > Best > > Francesca > > > > > > On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > Hi Francesca > > > > can you send us an image that shows why you think it can be improved? > > > > cheers > > Bruce > > On > > Mon, 18 Feb 2019, Francesca Strappini wrote: > > > > > > > > External Email - Use Caution > > > > > > Thank you!Now the registration is better but still not perfect. > > Is there a way to improve it? > > > > > > Best > > > > > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> ha > > > scritto: > > > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 > > weighted? If so, > > > you should use --t2 instead of --t1 in bbregister > > > > > > On 2/14/19 2:18 PM, Francesca Strappini wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Hi Doug, > > > > > > > > Could you advise me about how to correctly run mri_vol2vol? > > > > The functional data did not get perfectly registered to > > the anatomy so > > > > I'm afraid I'm not running it correctly. > > > > > > > > Thanks! > > > > > > > > > > > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl > > > > > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu>>> ha > > > > scritto: > > > > > > > > Hi Francesca > > > > > > > > sorry, I defer to Doug on the details of mri_vol2vol. > > > > > > > > cheers > > > > Bruce > > > > > > > > On Tue, 12 Feb 2019, > > > > Francesca Strappini wrote: > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Thank you for the reply! > > > > > I run: > > > > > mri_vol2vol --reg register.dat --mov > > func_data.nii.gz --targ > > > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o > > > > func_data_registered2T1.n
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution I'll try to find some visual way to show what I mean, but it's really something mild and probably negligible. Do you know if is it possible with mri_vol2vol to give to all the runs that belong to the same subject the same system coordinates? So that each voxel across runs will have the same coordinates. I noticed that the transformation matrix is written in the header but it's not really applied to the data. Thank you! Best Francesca On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl wrote: > Hi Francesca > > can you send us an image that shows why you think it can be improved? > > cheers > Bruce > On > Mon, 18 Feb 2019, Francesca Strappini wrote: > > > > > External Email - Use Caution > > > > Thank you!Now the registration is better but still not perfect. Is there > a way to improve it? > > > > Best > > > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> ha > > scritto: > > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted? > If so, > > you should use --t2 instead of --t1 in bbregister > > > > On 2/14/19 2:18 PM, Francesca Strappini wrote: > > > > > > External Email - Use Caution > > > > > > Hi Doug, > > > > > > Could you advise me about how to correctly run mri_vol2vol? > > > The functional data did not get perfectly registered to the > anatomy so > > > I'm afraid I'm not running it correctly. > > > > > > Thanks! > > > > > > > > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl > > > mailto:fis...@nmr.mgh.harvard.edu>> > ha > > > scritto: > > > > > > Hi Francesca > > > > > > sorry, I defer to Doug on the details of mri_vol2vol. > > > > > > cheers > > > Bruce > > > > > > On Tue, 12 Feb 2019, > > > Francesca Strappini wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Thank you for the reply! > > > > I run: > > > > mri_vol2vol --reg register.dat --mov func_data.nii.gz > --targ > > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o > > > func_data_registered2T1.nii.gz --no-resample > > > > > > > > Then I checked the registration and it seems that the > original > > > run is better aligned to the T1 than > > > > the registered one. Maybe am I not running mri_vol2vol > correctly? > > > > > > > > Thanks! > > > > Best > > > > > > > > > > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl > > > fis...@nmr.mgh.harvard.edu>> > > > ha scritto: > > > > Hi Francesca > > > > > > > > check out the --no-resample option in mri_vol2vol. > It just > > > changes the > > > > header, so I think should do what you want. > > > > > > > > cheers > > > > Bruce > > > > > > > > > > > > On Tue, 12 Feb 2019, Francesca Strappini wrote: > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Dear Freesurfer's experts, > > > > > > > > > > I would like to register some functional data to > the T1, > > > that were collected in > > > > separate days. > > > > > I used bbregister: > > > > > > > > > > bbregister --s sub3 --mov func_data.nii.gz - --reg > > > register.dat --init-coreg --t1 > > > > > > > > > > Now, I would like to resample the data based on the > > > register.dat without upsampling > > > > and keeping
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Thank you! Now the registration is better but still not perfect. Is there a way to improve it? Best Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted? If so, > you should use --t2 instead of --t1 in bbregister > > On 2/14/19 2:18 PM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > > > Could you advise me about how to correctly run mri_vol2vol? > > The functional data did not get perfectly registered to the anatomy so > > I'm afraid I'm not running it correctly. > > > > Thanks! > > > > > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu>> ha > > scritto: > > > > Hi Francesca > > > > sorry, I defer to Doug on the details of mri_vol2vol. > > > > cheers > > Bruce > > > > On Tue, 12 Feb 2019, > > Francesca Strappini wrote: > > > > > > > > External Email - Use Caution > > > > > > Thank you for the reply! > > > I run: > > > mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o > > func_data_registered2T1.nii.gz --no-resample > > > > > > Then I checked the registration and it seems that the original > > run is better aligned to the T1 than > > > the registered one. Maybe am I not running mri_vol2vol correctly? > > > > > > Thanks! > > > Best > > > > > > > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu>> > > ha scritto: > > > Hi Francesca > > > > > > check out the --no-resample option in mri_vol2vol. It just > > changes the > > > header, so I think should do what you want. > > > > > > cheers > > > Bruce > > > > > > > > > On Tue, 12 Feb 2019, Francesca Strappini wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Dear Freesurfer's experts, > > > > > > > > I would like to register some functional data to the T1, > > that were collected in > > > separate days. > > > > I used bbregister: > > > > > > > > bbregister --s sub3 --mov func_data.nii.gz - --reg > > register.dat --init-coreg --t1 > > > > > > > > Now, I would like to resample the data based on the > > register.dat without upsampling > > > and keeping the > > > > same FoV (3x3x3 mm; 64 64 50). Is it doable? > > > > > > > > Thanks! > > > > Best > > > > > > > > > > > > -- > > > > Francesca Strappini, Ph.D. > > > > Neurobiology Department > > > > Weizmann Institute of Science > > > > 234 Herzl Street, Rehovot 7610001 Israel > > > > Tel.: +972 58 444 2584 > > > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > > >_______ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- > > > Francesca Strappini, Ph.D. > > > Neurobiology Department > > > Weizmann Institute of Science > > > 234 Herzl Street, Rehovot 7610001 Israel > > > Tel.: +972 58 444 2584 > > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Hi Doug, Could you advise me about how to correctly run mri_vol2vol? The functional data did not get perfectly registered to the anatomy so I'm afraid I'm not running it correctly. Thanks! Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Francesca > > sorry, I defer to Doug on the details of mri_vol2vol. > > cheers > Bruce > > On Tue, 12 Feb 2019, > Francesca Strappini wrote: > > > > > External Email - Use Caution > > > > Thank you for the reply! > > I run: > > mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o > func_data_registered2T1.nii.gz --no-resample > > > > Then I checked the registration and it seems that the original run is > better aligned to the T1 than > > the registered one. Maybe am I not running mri_vol2vol correctly? > > > > Thanks! > > Best > > > > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl < > fis...@nmr.mgh.harvard.edu> ha scritto: > > Hi Francesca > > > > check out the --no-resample option in mri_vol2vol. It just changes > the > > header, so I think should do what you want. > > > > cheers > > Bruce > > > > > > On Tue, 12 Feb 2019, Francesca Strappini wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Freesurfer's experts, > > > > > > I would like to register some functional data to the T1, that > were collected in > > separate days. > > > I used bbregister: > > > > > > bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat > --init-coreg --t1 > > > > > > Now, I would like to resample the data based on the register.dat > without upsampling > > and keeping the > > > same FoV (3x3x3 mm; 64 64 50). Is it doable? > > > > > > Thanks! > > > Best > > > > > > > > > -- > > > Francesca Strappini, Ph.D. > > > Neurobiology Department > > > Weizmann Institute of Science > > > 234 Herzl Street, Rehovot 7610001 Israel > > > Tel.: +972 58 444 2584 > > > E-mail: francesca.strapp...@weizmann.ac.il > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] partial FoV - registration failure
External Email - Use Caution Thank you! Unfortunately, I don't have any whole brain scan. I registered the template and all the runs with tkregisterfv and the I run bbregsiter. Now, should I just re-run selxavg3-sess? Thanks Best Il giorno lun 26 nov 2018 alle ore 22:31 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > And you only have partial field of view fmri data on that day? No whole > brain localizer? Really, any whole-brain volume will do. If you do not, > then you'll have to initialize the bbr registration by hand, which is a > bit of a pain. You'd run something like > tkregisterfv --mov template.nii.gz --init-header --reg manual.reg.lta > --surfs > Then adjust the registration to be within 5mm of being right. Then run > bbregister using that registration as the --init-reg > If you have other scans where you have both the partial FoV and a whole > brain, you might be able to get an init reg by registering the partial > FoVs from different days. > good luck > > > > On 11/26/2018 03:19 PM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Thanks for the fast reply! > > > > Unfortunately, I have only 3 mprage scans that were collected in > > another day but no whole-head functional data. > > > > Il giorno lun 26 nov 2018 alle ore 22:07 Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> ha scritto: > > > > Do you have any scan that was acquired at the same time that is whole > > head? Any scan will do. If so, you can run register-sess using the > > -bbr-int option (or bbregister directly). Eg, if the anatomical was > > acquired at the same time, then, to use register-sess, create a > > folder > > in the session folder called anatomical/001 and put the anatomical in > > there (eg, anat.nii.gz), then use -bbr-int anatomical anat > > > > > > On 11/26/2018 02:58 PM, Francesca Strappini wrote: > > > > > > External Email - Use Caution > > > > > > Dear freesurfer experts, > > > > > > I am using freesurfer to analyze some fMRI data collected on two > > > monkeys. My runs have a partial field of view, since just the > > > posterior part of the brain was scanned. Unfortunately, no > > full-head > > > EPI was collected. The registration between the processed > > functional > > > data and the T1 is bad. All the values in the register.dof6.mincost > > > file are above 0.8 and also visually I can see some mismatch. I > > though > > > to run bbregister, could you suggest me which is the best procedure > > > and which steps of the preprocessing I should re-run after? > > > > > > Thanks > > > > > > -- > > > Francesca Strappini, Ph.D. > > > Neurobiology Department > > > Weizmann Institute of Science > > > 234 Herzl Street, Rehovot 7610001 Israel > > > Tel.: +972 58 444 2584 > > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > <mailto:francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il>> > > > > > > > > > _______ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_segstat: same output with two different label
External Email - Use Caution Thanks! There was a mistake in the contrasts indeed. Best Il giorno lun 11 feb 2019 alle ore 18:59 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > > If mri_diff says that there is no difference, then there is something > wrong. Double check that your contrasts are correct. > > > On 2/10/19 9:47 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Thanks a lot for the reply! > > If I run mri_diff order/z.nii.gz disorder/z.nii.gz I indeed get zero. > > However, if I perform the contrast "order minus disorder" I get 0.1, > > so I should see some difference although very small, right? > > These are the outputs: > > > > francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ > > > mri_segstats --i order/z.nii.gz --slabel AB lh > > /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg > > lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum > > > > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ > > cwd > > cmdline mri_segstats --i order/z.nii.gz --slabel AB lh > > /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg > > lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum > > sysname Linux > > hostname francesca-desktop > > machine x86_64 > > user francesca > > UseRobust 0 > > Constructing seg from label > > Loading order/z.nii.gz > > Vertex Area is 0.65781 mm^3 > > Generating list of segmentation ids > > Found 2 segmentations > > Computing statistics for each segmentation > > > > Reporting on 2 segmentations > > Using PrintSegStat > > Computing spatial average of each frame > > 0 1 > > Writing to lh.V2dorsal_AB_order_avg > > 0 -0.950279 > > 1 1.31525 > > mri_segstats done > > > > francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ > > > mri_segstats --i disorder/z.nii.gz --slabel AB lh > > /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg > > lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum > > > > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ > > cwd > > cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh > > /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg > > lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum > > sysname Linux > > hostname francesca-desktop > > machine x86_64 > > user francesca > > UseRobust 0 > > Constructing seg from label > > Loading disorder/z.nii.gz > > Vertex Area is 0.65781 mm^3 > > Generating list of segmentation ids > > Found 2 segmentations > > Computing statistics for each segmentation > > > > Reporting on 2 segmentations > > Using PrintSegStat > > Computing spatial average of each frame > > 0 1 > > Writing to lh.V2dorsal_AB_disorder_avg > > 0 -0.950279 > > 1 1.31525 > > mri_segstats done > > > > mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh > > /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg > > lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum > > lh.V2dorsal_AB_orderVsdisorder_sum > > > > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ > > cwd > > cmdline mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh > > /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg > > lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum > > lh.V2dorsal_AB_orderVsdisorder_sum > > sysname Linux > > hostname francesca-desktop > > machine x86_64 > > user francesca > > UseRobust 0 > > Constructing seg from label > > Loading order-vs-disorder/z.nii.gz > > Vertex Area is 0.65781 mm^3 > > Generating list of segmentation ids > > Found 2 segmentations > > Computing statistics for each segmentation > > > > Reporting on 2 segmentations > > Using PrintSegStat > > Computing spatial average of each frame > > 0 1 > > Writing to lh.V2dorsal_AB_orderVsdisorder_avg > > 0 0.119339 > > 1 -1.93788 > > mri_segstats done > > > > Thanks again for the help! > > Best > > Francesca > > > > > > > > Il giorno mar 22 gen 2019 alle ore 20:55 Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> ha scritto: > > > > I don't know what is happening. If the two z-maps are really > > different, > >
Re: [Freesurfer] registration and resampling in native space
External Email - Use Caution Thank you for the reply! I run: mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o func_data_registered2T1.nii.gz --no-resample Then I checked the registration and it seems that the original run is better aligned to the T1 than the registered one. Maybe am I not running mri_vol2vol correctly? Thanks! Best Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Francesca > > check out the --no-resample option in mri_vol2vol. It just changes the > header, so I think should do what you want. > > cheers > Bruce > > > On Tue, 12 Feb 2019, Francesca Strappini wrote: > > > > > External Email - Use Caution > > > > Dear Freesurfer's experts, > > > > I would like to register some functional data to the T1, that were > collected in separate days. > > I used bbregister: > > > > bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat > --init-coreg --t1 > > > > Now, I would like to resample the data based on the register.dat without > upsampling and keeping the > > same FoV (3x3x3 mm; 64 64 50). Is it doable? > > > > Thanks! > > Best > > > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] registration and resampling in native space
External Email - Use Caution Dear Freesurfer's experts, I would like to register some functional data to the T1, that were collected in separate days. I used bbregister: bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat --init-coreg --t1 Now, I would like to resample the data based on the register.dat without upsampling and keeping the same FoV (3x3x3 mm; 64 64 50). Is it doable? Thanks! Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_segstat: same output with two different label
External Email - Use Caution Thanks a lot for the reply! If I run mri_diff order/z.nii.gz disorder/z.nii.gz I indeed get zero. However, if I perform the contrast "order minus disorder" I get 0.1, so I should see some difference although very small, right? These are the outputs: francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ mri_segstats --i order/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i order/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum sysname Linux hostname francesca-desktop machine x86_64 user francesca UseRobust 0 Constructing seg from label Loading order/z.nii.gz Vertex Area is 0.65781 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 2 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 Writing to lh.V2dorsal_AB_order_avg 0 -0.950279 1 1.31525 mri_segstats done francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ mri_segstats --i disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum sysname Linux hostname francesca-desktop machine x86_64 user francesca UseRobust 0 Constructing seg from label Loading disorder/z.nii.gz Vertex Area is 0.65781 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 2 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 Writing to lh.V2dorsal_AB_disorder_avg 0 -0.950279 1 1.31525 mri_segstats done mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum lh.V2dorsal_AB_orderVsdisorder_sum $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum lh.V2dorsal_AB_orderVsdisorder_sum sysname Linux hostname francesca-desktop machine x86_64 user francesca UseRobust 0 Constructing seg from label Loading order-vs-disorder/z.nii.gz Vertex Area is 0.65781 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 2 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 Writing to lh.V2dorsal_AB_orderVsdisorder_avg 0 0.119339 1 -1.93788 mri_segstats done Thanks again for the help! Best Francesca Il giorno mar 22 gen 2019 alle ore 20:55 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > I don't know what is happening. If the two z-maps are really different, > then it should have given different values. Run this > mri_diff order/z.nii.gz disorder/z.nii.gz > Does it indicate that there is a difference? If so, can you run your two > mri_segment commands and send me the terminal output of each? > As for the two mean intensity values, one (Seg0001) is from inside your > ROI and the other (Seg) is outside. You can have it exclude Seg > with --excludeid 0 > > > On 1/20/19 10:00 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer's experts, > > > > I'm trying to run a ROIs mean intensity analysis using mri_segstat. > > I'm using as an input contrast maps created with mkcontrast-sess and > > selxavg3-sess (block-design experiment) and as masks, some labels > > created on the surface with a retinotopic analysis. > > > > I noticed that all my outputs with the same label have the same > > values, regardless of the contrast map that I'm giving as an input. > > However, if I plot the contrast maps on the surface I can clearly see > > that there are differences, so also the mean signal should be different. > > > > Maybe I'm not running the command correctly: > > > > mri_segstats --i z.nii.gz --slabel sub1 lh lh.V2dorsal_sub1.label > > --sfavg lh.V2dorsal_sub1_condition1_avg --snr --sum > > lh.V2dorsal_sub1_condition1_sum > > > > These are two outputs from the same regions but with two differe
Re: [Freesurfer] partial FoV - registration failure
External Email - Use Caution Thanks for the fast reply! Unfortunately, I have only 3 mprage scans that were collected in another day but no whole-head functional data. Il giorno lun 26 nov 2018 alle ore 22:07 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > Do you have any scan that was acquired at the same time that is whole > head? Any scan will do. If so, you can run register-sess using the > -bbr-int option (or bbregister directly). Eg, if the anatomical was > acquired at the same time, then, to use register-sess, create a folder > in the session folder called anatomical/001 and put the anatomical in > there (eg, anat.nii.gz), then use -bbr-int anatomical anat > > > On 11/26/2018 02:58 PM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Dear freesurfer experts, > > > > I am using freesurfer to analyze some fMRI data collected on two > > monkeys. My runs have a partial field of view, since just the > > posterior part of the brain was scanned. Unfortunately, no full-head > > EPI was collected. The registration between the processed functional > > data and the T1 is bad. All the values in the register.dof6.mincost > > file are above 0.8 and also visually I can see some mismatch. I though > > to run bbregister, could you suggest me which is the best procedure > > and which steps of the preprocessing I should re-run after? > > > > Thanks > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] partial FoV - registration failure
External Email - Use Caution Dear freesurfer experts, I am using freesurfer to analyze some fMRI data collected on two monkeys. My runs have a partial field of view, since just the posterior part of the brain was scanned. Unfortunately, no full-head EPI was collected. The registration between the processed functional data and the T1 is bad. All the values in the register.dof6.mincost file are above 0.8 and also visually I can see some mismatch. I though to run bbregister, could you suggest me which is the best procedure and which steps of the preprocessing I should re-run after? Thanks -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer selxavg3-sess error
External Email - Use Caution Thank you! I changed the event file and re-run the analysis. I got an error message when creating the contrast: mkanalysis-sess -analysis FF-MonkeyCassis-event.sm03.lh -surface MonkeyCassis lh -fwhm 3 -fsd bold -per-run -event-related -paradigm FF.par -TR 2 -nconditions 2 -refeventdur 16 -spmhrf mkcontrast-sess -analysis FF-MonkeyCassis-event.sm03.lh -contrast coherent-v-random -a 1 -c 2 @: Missing file name. INFO: Found 1 Non-Null Conditions INFO: Found Delays ERROR: Condition ID 2 out of range (0:1) 21161coherent 162161random 321161coherent 482161random 641161coherent 822161random 961161coherent 1122161random 1281161coherent 1442161random 1621161coherent 1762161random 1921161coherent 2282161random 2241161coherent 2422161random Thanks a lot for the help! Best Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer selxavg3-sess error
External Email - Use Caution Thanks! Now it's loading correctly my event file. However, when I run selxavg3-sess I get this error message: selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF -no-con-ok outanadir = /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF/bold/FF-MonkeyCassis.sm03.lh Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points Excluding 2 points parfiles condition id list: 1 ERROR: found 1 non-null conditions, expected 2 -- ERROR: fast_selxavg3() failed\n This is my even file: 01321ON 320321OFF 641321ON 960321OFF 1281321ON 1600321OFF 1921321ON 2240321OFF Thanks for the help! Best Francesca Il giorno gio 3 mag 2018 alle ore 00:49 Douglas N. Greve < dgr...@mgh.harvard.edu> ha scritto: > oops, sorry. Looks like it is having a problem loading your paradigm > file. Check that. If the error does not pop out to you then send it to me. > > > On 05/02/2018 10:06 AM, Francesca Strappini wrote: > > Hi, sorry, maybe my last email got lost. Is there anything I can try > > to fix this problem with selxavg3-sess? > > > > Thanks! > > Best > > Francesca > > > > 2018-04-24 20:35 GMT+03:00 Francesca Strappini > > mailto:francescastrapp...@gmail.com>>: > > > > Thank you for the reply! > > I deleted the contrasts and run this command line: > > > > selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF > -no-con-ok > > > > > > --- matlab output > > MATLAB is selecting SOFTWARE OPENGL rendering. > > > > < M A T L A B (R) > > > Copyright 1984-2016 The MathWorks, Inc. > >R2016b (9.1.0.441655) 64-bit (glnxa64) > > September 7, 2016 > > > > > > To get started, type one of these: helpwin, helpdesk, or demo. > > For product information, visit www.mathworks.com > > <http://www.mathworks.com>. > > > > >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > >> /usr/local/freesurfer/matlab/MRIread.m > > >> >> >> starting fast_selxavg3b > > > > > > #@# MonkeyCassis-FF ### > > /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF > > - > > $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ > > - > > outtop = /usr/local/freesurfer/fsfast/Monkeys > > Extension format = nii.gz > > INFO: key nSliceGroups unrecognized, line 11, skipping > > Subscripted assignment dimension mismatch. > > > > Error in fast_ldpar4 (line 97) > > par4(nthrow,1) = tonset; > > > > Error in flac_customize (line 121) > > [par partype] = fast_ldpar4(parpath); > > > > Error in fast_selxavg3b (line 129) > > flac0 = flac_customize(flac0); > > > > >> -- > > ERROR: fast_selxavg3() failed\n > > > > > > 2018-04-24 20:27 GMT+03:00 Douglas Greve > <mailto:dgr...@mgh.harvard.edu>>: > > > > Try deleting the contrasts (.mat files) and rerunning > > > > > > On 4/24/18 5:48 AM, Francesca Strappini wrote: > >> > >> > >> Dear FreeSurfer experts, > >> > >> I'm trying to analyze some monkey functional data. I got this > >> error message with selxavg3-sess. > >> > >> I run the following commands: > >> > >> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast > >> ON-vs-OFF -a 1 -c 0 > >> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast > >> ON-vs-OFF -a 1 -c 0 > >> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s > >> MonkeyCassis-FF -fsd bold -per-session > >> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF > >> > >> > >> --- matlab output > >> MATLAB is selecting SOFTWARE OPENGL rendering. > >> > >>
Re: [Freesurfer] selxavg3-sess contrasts error
External Email - Use Caution Thank you! It was a format problem. Best Francesca Il giorno mer 22 ago 2018 alle ore 17:51 Douglas N. Greve < dgr...@mgh.harvard.edu> ha scritto: > There is something wrong with the paradigm file (-par when running > mkanalysis-sess). Check the paradigm file for this subject and run. > > On 08/22/2018 10:16 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Hi, > > > > I'm trying to analyze a block-design experiment. I run selxavg3-sess: > > > > selxavg3-sess -s MS -analysis MS_VisLocDrawings.sm03.rh > > > > And I got this error message while computing the contrasts. Any idea > > what does it mean? > > > > > > outtop = /home/labs/malach/frastra/freesurfer/fsfast/visloc_drawing > > Extension format = nii.gz > > 1 animals-vs-fixation.mat > > 2 body_parts-vs-fixation.mat > > 3 faces-vs-fixation.mat > > 4 houses-vs-fixation.mat > > 5 scrambled_images-vs-fixation.mat > > 6 tools-vs-fixation.mat > > Unable to perform assignment because the indices on the left side are not > > compatible with the size of the right side. > > > > Error in fast_ldpar4 (line 97) > > par4(nthrow,1) = tonset; > > > > Error in flac_customize (line 121) > > [par partype] = fast_ldpar4(parpath); > > > > Error in fast_selxavg3 (line 65) > > flac0 = flac_customize(flac0); > > > > >> -- > > ERROR: fast_selxavg3() failed\n > > > > > > Thank you! > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] selxavg3-sess contrasts error
External Email - Use Caution Hi, I'm trying to analyze a block-design experiment. I run selxavg3-sess: selxavg3-sess -s MS -analysis MS_VisLocDrawings.sm03.rh And I got this error message while computing the contrasts. Any idea what does it mean? outtop = /home/labs/malach/frastra/freesurfer/fsfast/visloc_drawing Extension format = nii.gz 1 animals-vs-fixation.mat 2 body_parts-vs-fixation.mat 3 faces-vs-fixation.mat 4 houses-vs-fixation.mat 5 scrambled_images-vs-fixation.mat 6 tools-vs-fixation.mat Unable to perform assignment because the indices on the left side are not compatible with the size of the right side. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you! -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer selxavg3-sess error
External Email - Use Caution Hi, sorry, maybe my last email got lost. Is there anything I can try to fix this problem with selxavg3-sess? Thanks! Best Francesca 2018-04-24 20:35 GMT+03:00 Francesca Strappini <francescastrapp...@gmail.com >: > Thank you for the reply! > I deleted the contrasts and run this command line: > > selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok > > > --- matlab output > MATLAB is selecting SOFTWARE OPENGL rendering. > > < M A T L A B (R) > > Copyright 1984-2016 The MathWorks, Inc. >R2016b (9.1.0.441655) 64-bit (glnxa64) > September 7, 2016 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > > >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > >> /usr/local/freesurfer/matlab/MRIread.m > >> >> >> starting fast_selxavg3b > > > #@# MonkeyCassis-FF ### > /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF > - > $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ > - > outtop = /usr/local/freesurfer/fsfast/Monkeys > Extension format = nii.gz > INFO: key nSliceGroups unrecognized, line 11, skipping > Subscripted assignment dimension mismatch. > > Error in fast_ldpar4 (line 97) > par4(nthrow,1) = tonset; > > Error in flac_customize (line 121) > [par partype] = fast_ldpar4(parpath); > > Error in fast_selxavg3b (line 129) > flac0 = flac_customize(flac0); > > >> ------ > ERROR: fast_selxavg3() failed\n > > > 2018-04-24 20:27 GMT+03:00 Douglas Greve <dgr...@mgh.harvard.edu>: > >> Try deleting the contrasts (.mat files) and rerunning >> >> On 4/24/18 5:48 AM, Francesca Strappini wrote: >> >> >> Dear FreeSurfer experts, >> >> I'm trying to analyze some monkey functional data. I got this error >> message with selxavg3-sess. >> >> I run the following commands: >> >> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a >> 1 -c 0 >> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a >> 1 -c 0 >> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd >> bold -per-session >> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF >> >> >> --- matlab output >> MATLAB is selecting SOFTWARE OPENGL rendering. >> >> < M A T L A B (R) > >> Copyright 1984-2016 The MathWorks, Inc. >>R2016b (9.1.0.441655) 64-bit (glnxa64) >> September 7, 2016 >> >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com. >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> >> /usr/local/freesurfer/matlab/MRIread.m >> >> >> >> starting fast_selxavg3b >> >> >> #@# MonkeyCassis-FF ### >> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF >> - >> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ >> - >> outtop = /usr/local/freesurfer/fsfast/Monkeys >> Extension format = nii.gz >> INFO: key nSliceGroups unrecognized, line 11, skipping >> 1 ON-vs-OFF.mat >> Subscripted assignment dimension mismatch. >> >> Error in fast_ldpar4 (line 97) >> par4(nthrow,1) = tonset; >> >> Error in flac_customize (line 121) >> [par partype] = fast_ldpar4(parpath); >> >> Error in fast_selxavg3b (line 129) >> flac0 = flac_customize(flac0); >> >> >> -- >> ERROR: fast_selxavg3() failed\n >> >> Thank you! >> Best >> >> Francesca >> >> -- >> Francesca Strappini, Ph.D. >> Neurobiology Department >> Weizmann Institute of Science >> 234 Herzl Street, Rehovot 7610001 Israel >> Tel.: +972 58 444 2584 >> E-mail: francesca.strapp...@weizmann.ac.il >> >> >> ___ >> Freesurfer mailing >>
Re: [Freesurfer] freesurfer selxavg3-sess error
External Email - Use Caution Thank you for the reply! I deleted the contrasts and run this command line: selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok --- matlab output MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2016 The MathWorks, Inc. R2016b (9.1.0.441655) 64-bit (glnxa64) September 7, 2016 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# MonkeyCassis-FF ### /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF - $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ - outtop = /usr/local/freesurfer/fsfast/Monkeys Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n 2018-04-24 20:27 GMT+03:00 Douglas Greve <dgr...@mgh.harvard.edu>: > Try deleting the contrasts (.mat files) and rerunning > > On 4/24/18 5:48 AM, Francesca Strappini wrote: > > > Dear FreeSurfer experts, > > I'm trying to analyze some monkey functional data. I got this error > message with selxavg3-sess. > > I run the following commands: > > mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 > -c 0 > mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1 > -c 0 > preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd > bold -per-session > selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF > > > --- matlab output > MATLAB is selecting SOFTWARE OPENGL rendering. > > < M A T L A B (R) > > Copyright 1984-2016 The MathWorks, Inc. >R2016b (9.1.0.441655) 64-bit (glnxa64) > September 7, 2016 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > > >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > >> /usr/local/freesurfer/matlab/MRIread.m > >> >> >> starting fast_selxavg3b > > > #@# MonkeyCassis-FF ### > /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF > - > $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ > - > outtop = /usr/local/freesurfer/fsfast/Monkeys > Extension format = nii.gz > INFO: key nSliceGroups unrecognized, line 11, skipping > 1 ON-vs-OFF.mat > Subscripted assignment dimension mismatch. > > Error in fast_ldpar4 (line 97) > par4(nthrow,1) = tonset; > > Error in flac_customize (line 121) > [par partype] = fast_ldpar4(parpath); > > Error in fast_selxavg3b (line 129) > flac0 = flac_customize(flac0); > > >> -- > ERROR: fast_selxavg3() failed\n > > Thank you! > Best > > Francesca > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the
[Freesurfer] freesurfer selxavg3-sess error
External Email - Use Caution Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 -c 0 mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1 -c 0 preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd bold -per-session selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF --- matlab output MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2016 The MathWorks, Inc. R2016b (9.1.0.441655) 64-bit (glnxa64) September 7, 2016 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# MonkeyCassis-FF ### /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF - $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ - outtop = /usr/local/freesurfer/fsfast/Monkeys Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping 1 ON-vs-OFF.mat Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] make_average_subject monkey data
That worked! Thanks a lot :) I suppose that I could improve the appearance with some further manual editing of the surfaces. Best Francesca 2018-03-16 16:17 GMT+01:00 Douglas Greve <dgr...@mgh.harvard.edu>: > Try this: > > 1. make a back up of the talairach.xfm > > cp talairach.xfm bak.talarach.xfm > > 2. Convert the lta to an xfm: > > tkregister --mov ../orig.mgz --lta talairach.lta --reg deleteme.reg.dat > --xfmout talairach.xfm --s fsaverage --surfs --noedit > > 3. rerun make_average_subject > > On 3/16/18 5:24 AM, Francesca Strappini wrote: > > Thanks Doug! > Actually talairach.lta looks quite good. However, when I tried to > make_average_subject with --xform talairach.lta I got immediately an > error: > > make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey > --xform talairach.lta > > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > /usr/local/freesurfer/bin/make_average_subject --subjects MonkeyCelia > MonkeyCassis --out AVGmonkey --xform talairach.lta > > $Id: make_average_subject,v 1.23.2.1 2016/08/02 21:20:04 greve Exp $ > Fri Mar 16 10:20:30 CET 2018 > /usr/local/freesurfer/subjects > output ddir is /usr/local/freesurfer/subjects > uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm), > 24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare) > make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey > --xform talairach.lta > > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > /usr/local/freesurfer/bin/make_average_surface --subjects MonkeyCelia > MonkeyCassis --out AVGmonkey --xform talairach.lta > > $Id: make_average_surface,v 1.62 2016/02/16 17:17:20 zkaufman Exp $ > Fri Mar 16 10:20:30 CET 2018 > /usr/local/freesurfer/subjects/AVGmonkey > output ddir is /usr/local/freesurfer/subjects > uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm), > 24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare) > > make_average_surface > > Fri Mar 16 10:20:30 CET 2018 > /usr/local/freesurfer/subjects/AVGmonkey > /usr/local/freesurfer/bin/make_average_surface > --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta > input subjects: MonkeyCelia MonkeyCassis > output subject: AVGmonkey > mri_add_xform_to_header -c auto /usr/local/freesurfer/ > subjects/AVGmonkey/mri/mni305.cor.mgz /usr/local/freesurfer/ > subjects/AVGmonkey/mri/mni305.cor.mgz > INFO: extension is mgz > > #@# Making lh registration template - > /usr/local/freesurfer/subjects/AVGmonkey > mris_make_template -norot -annot aparc lh sphere.reg MonkeyCelia > MonkeyCassis lh.reg.template.tif > not aligning hemispheres before averaging. > zeroing medial wall in aparc > creating new parameterization... > > processing subject MonkeyCelia (1 of 2) > reading spherical surface /usr/local/freesurfer/ > subjects/MonkeyCelia/surf/lh.sphere.reg... > reading colortable from annotation file... > colortable with 36 entries read (originally /autofs/space/tanha_002/users/ > greve/fsdev.build/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface /usr/local/freesurfer/ > subjects/MonkeyCelia/surf/lh.inflated.H... > curvature mean = -0.074, std = 1.020 > computing parameterization for surface /usr/local/freesurfer/ > subjects/MonkeyCelia/surf/lh.sulc... > computing parameterization for surface /usr/local/freesurfer/ > subjects/MonkeyCelia/surf/lh.smoothwm... > > processing subject MonkeyCassis (2 of 2) > reading spherical surface /usr/local/freesurfer/ > subjects/MonkeyCassis/surf/lh.sphere.reg... > curvature mean = -0.041, std = 3.478 > curvature mean = -0.056, std = 0.439 > reading colortable from annotation file... > colortable with 36 entries read (originally /autofs/space/tanha_002/users/ > greve/fsdev.build/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface /usr/local/freesurfer/ > subjects/MonkeyCassis/surf/lh.inflated.H... > curvature mean = -0.048, std = 1.029 > computing parameterization for surface /usr/local/freesurfer/ > subjects/MonkeyCassis/surf/lh.sulc... > computing parameterization for surface /usr/local/freesurfer/ > subjects/MonkeyCassis/surf/lh.smoothwm... > writing updated template with 2 subjects to lh.reg.template.tif... > curvature mean = 0.038, std = 4.146 > curvature mean = -0.062, std = 0.305 > > #@# Making rh registration template - > /usr/local/freesurfer/subjects/AVGmonkey > mris_make_template -norot -annot aparc rh sphere.reg MonkeyCelia > MonkeyCassis rh.reg.template.tif > not aligning hemispheres before averaging. >
Re: [Freesurfer] make_average_subject monkey data
/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.inflated.H... curvature mean = -0.059, std = 1.018 computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.sulc... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.smoothwm... writing updated template with 2 subjects to rh.reg.template.tif... curvature mean = 0.036, std = 4.168 curvature mean = -0.068, std = 0.371 #@# Making average lh.white surface - Fri Mar 16 10:20:34 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey mris_make_average_surface -X talairach.lta -i 7 -o white -sdir-out /usr/local/freesurfer/subjects lh white sphere.reg AVGmonkey MonkeyCelia MonkeyCassis using xform talairach.lta... reading vertex positions from white... --- hemi= lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = AVGmonkey xform = talairach.lta --- --- #@# processing subject 1/2 MonkeyCelia... Reading /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sphere.reg Read /usr/local/freesurfer/subjects/MonkeyCelia/mri/T1.mgz Surface area: 86.0 cm^2 ERROR: don't know what to do with talairach.lta mris_average_surface failed ERROR: make_average_surface 2018-03-15 23:18 GMT+01:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > See if the talairach.lta is any better, eg > > cd subject/mri/transforms > > tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta > > If so, you can try running make_average_subject with --xform talairach.lta > > I've never done this, but it might work :) > > > > On 03/15/2018 01:02 PM, Francesca Strappini wrote: > > Thank you, Doug! > > One monkey has a pretty decent registration while the other one does > > not even appear in the window when I try to manually check the > > registration with this command line: > > tkregister --mgz --s MonkeyCelia --fstal --surf orig > > It looks like if there is no brain. > > > > 2018-03-15 16:57 GMT+01:00 Douglas N. Greve <dgr...@mgh.harvard.edu > > <mailto:dgr...@mgh.harvard.edu>>: > > > > Check the talairach.xfm registration. It is probably way off. It does > > not have to be perfect (esp since they are different species), but > the > > two subjects should have a similar registration > > > > > > On 03/14/2018 07:27 PM, Francesca Strappini wrote: > > > Both average hemispheres look very bad, they don't even look like a > > > brain. The two monkey surfaces look reasonable, except for some > > > topological defect that I think could be fixed with some manual > > > editing. Is there anything I could try? > > > > > > Thanks a lot > > > Francesca > > > > > > 2018-03-14 23:41 GMT+01:00 Douglas N. Greve > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>: > > > > > > I don't know what is going on there except that the average > > > surfaces are > > > probably wrong in some way. It looks like it made it all the > way > > > through > > > except for that step, so all of the output should be there. How > > > does it > > > look? > > > > > > > > > On 03/13/2018 05:27 PM, Francesca Strappini wrote: > > > > Dear Experts, > > > > > > > > I'm trying to average two monkey brains. I run this > > command line: > > > > > > > > make_average_subject --subjects MonkeyCelia MonkeyCassis > > --out > > > AVGmonkeys > > > > > > > > but it ended with errors. > > > > > > > > I run the recon-all for both monkyes with the option > > -notal-check > > > > because I had problems with the Talairach registration. I > > don't know > > > > if this could be the cause. > > > > > > > > Thanks a lot > > > > Francesca > > > > > > > > Tue Mar 13 20:04:06 CET 2018 > > > > /usr/local/freesurfer/subjects/AVGmonkeys > > > > /usr/local/freesurfer/bin/recon-all > >
Re: [Freesurfer] make_average_subject monkey data
Thank you, Doug! One monkey has a pretty decent registration while the other one does not even appear in the window when I try to manually check the registration with this command line: tkregister --mgz --s MonkeyCelia --fstal --surf orig It looks like if there is no brain. 2018-03-15 16:57 GMT+01:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > Check the talairach.xfm registration. It is probably way off. It does > not have to be perfect (esp since they are different species), but the > two subjects should have a similar registration > > > On 03/14/2018 07:27 PM, Francesca Strappini wrote: > > Both average hemispheres look very bad, they don't even look like a > > brain. The two monkey surfaces look reasonable, except for some > > topological defect that I think could be fixed with some manual > > editing. Is there anything I could try? > > > > Thanks a lot > > Francesca > > > > 2018-03-14 23:41 GMT+01:00 Douglas N. Greve <dgr...@mgh.harvard.edu > > <mailto:dgr...@mgh.harvard.edu>>: > > > > I don't know what is going on there except that the average > > surfaces are > > probably wrong in some way. It looks like it made it all the way > > through > > except for that step, so all of the output should be there. How > > does it > > look? > > > > > > On 03/13/2018 05:27 PM, Francesca Strappini wrote: > > > Dear Experts, > > > > > > I'm trying to average two monkey brains. I run this command line: > > > > > > make_average_subject --subjects MonkeyCelia MonkeyCassis --out > > AVGmonkeys > > > > > > but it ended with errors. > > > > > > I run the recon-all for both monkyes with the option -notal-check > > > because I had problems with the Talairach registration. I don't > know > > > if this could be the cause. > > > > > > Thanks a lot > > > Francesca > > > > > > Tue Mar 13 20:04:06 CET 2018 > > > /usr/local/freesurfer/subjects/AVGmonkeys > > > /usr/local/freesurfer/bin/recon-all > > > -s AVGmonkeys -cortribbon -aparc2aseg > > > subjid AVGmonkeys > > > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > > > FREESURFER_HOME /usr/local/freesurfer > > > Actual FREESURFER_HOME /usr/local/freesurfer > > > build-stamp.txt: > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 > 21:23:04 > > > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > > > cputime unlimited > > > filesize unlimited > > > datasize unlimited > > > stacksize8192 kbytes > > > coredumpsize 0 kbytes > > > memoryuseunlimited > > > vmemoryuse unlimited > > > descriptors 1024 > > > memorylocked 64 kbytes > > > maxproc 63682 > > > maxlocks unlimited > > > maxsignal63682 > > > maxmessage 819200 > > > maxnice 0 > > > maxrtprio0 > > > maxrttimeunlimited > > > > > > totalusedfree shared buff/cache > > > available > > > Mem: 16350220 4943572 7520800 278988 3885848 > > > 10739864 > > > Swap: 19528700 019528700 > > > > > > > > > program versions used > > > $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ > > > $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman > > Exp $ > > > mri_convert.bin -all-info > > > ProgramName: mri_convert.bin ProgramArguments: -all-info > > > ProgramVersion: $Name: stable6 $ TimeStamp: > > 2018/03/13-19:04:06-GMT > > > BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v > > 1.226 > > > 2016/02/26 16:15:24 mreuter Exp $ User: francesca Machine: > shalimpc > > > Platform: Linux PlatformVersion: 4.4.0-116-generic > > CompilerName: GCC > > > CompilerVersion: 40400 > > > FLIRT version 5.5 > > > $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ > > > mri_convert.bin --version > > > stable6 > > > ProgramName: tkregister2_cmdl ProgramArguments: --all-info > > > ProgramV
Re: [Freesurfer] make_average_subject monkey data
Both average hemispheres look very bad, they don't even look like a brain. The two monkey surfaces look reasonable, except for some topological defect that I think could be fixed with some manual editing. Is there anything I could try? Thanks a lot Francesca 2018-03-14 23:41 GMT+01:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > I don't know what is going on there except that the average surfaces are > probably wrong in some way. It looks like it made it all the way through > except for that step, so all of the output should be there. How does it > look? > > > On 03/13/2018 05:27 PM, Francesca Strappini wrote: > > Dear Experts, > > > > I'm trying to average two monkey brains. I run this command line: > > > > make_average_subject --subjects MonkeyCelia MonkeyCassis --out > AVGmonkeys > > > > but it ended with errors. > > > > I run the recon-all for both monkyes with the option -notal-check > > because I had problems with the Talairach registration. I don't know > > if this could be the cause. > > > > Thanks a lot > > Francesca > > > > Tue Mar 13 20:04:06 CET 2018 > > /usr/local/freesurfer/subjects/AVGmonkeys > > /usr/local/freesurfer/bin/recon-all > > -s AVGmonkeys -cortribbon -aparc2aseg > > subjid AVGmonkeys > > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > > FREESURFER_HOME /usr/local/freesurfer > > Actual FREESURFER_HOME /usr/local/freesurfer > > build-stamp.txt: freesurfer-Linux-centos6_x86_ > 64-stable-pub-v6.0.0-2beb96c > > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 > > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > > cputime unlimited > > filesize unlimited > > datasize unlimited > > stacksize8192 kbytes > > coredumpsize 0 kbytes > > memoryuseunlimited > > vmemoryuse unlimited > > descriptors 1024 > > memorylocked 64 kbytes > > maxproc 63682 > > maxlocks unlimited > > maxsignal63682 > > maxmessage 819200 > > maxnice 0 > > maxrtprio0 > > maxrttimeunlimited > > > > totalusedfree shared buff/cache > > available > > Mem: 16350220 4943572 7520800 278988 3885848 > > 10739864 > > Swap: 19528700 019528700 > > > > > > program versions used > > $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ > > $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ > > mri_convert.bin -all-info > > ProgramName: mri_convert.bin ProgramArguments: -all-info > > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT > > BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 > > 2016/02/26 16:15:24 mreuter Exp $ User: francesca Machine: shalimpc > > Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > > CompilerVersion: 40400 > > FLIRT version 5.5 > > $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ > > mri_convert.bin --version > > stable6 > > ProgramName: tkregister2_cmdl ProgramArguments: --all-info > > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT > > BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v > > 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: francesca Machine: > > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > > CompilerName: GCC CompilerVersion: 40400 > > Program nu_correct, built from: > > Package MNI N3, version 1.12.0, compiled by nicks@terrier > > (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 > > ProgramName: mri_make_uchar ProgramArguments: -all-info > > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT > > BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 > > 2011/03/02 00:04:14 nicks Exp $ User: francesca Machine: shalimpc > > Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC > > CompilerVersion: 40400 > > ProgramName: mri_normalize ProgramArguments: -all-info > > ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT > > BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v > > 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: francesca Machine: > > shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic > > CompilerName: GCC CompilerVersion: 40400 > > ProgramName: mri_watershed ProgramArguments: -all-info > > ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT > > BuildTimeStamp: Jan 18 2017 16:38:58
[Freesurfer] make_average_subject monkey data
PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ### # #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AVGmonkeys SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 34535 writing volume /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz ERROR: ribbon has non-zero value at location 0,0,0 Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13 20:26:58 CET 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] niiRead error
It does work with 6.0, thank you! 2017-07-31 20:59 GMT+03:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > I think this may be fixed in 6.0 > > On 7/31/17 12:43 PM, Francesca Strappini wrote: > > Thanks for the reply. > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. > > I opened it with fslview and it looks like a normal 3-dimentional file. > > Thanks > Francesca > > 2017-07-31 16:38 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > >> what version of FS are you running? >> >> >> On 7/30/17 12:37 PM, Bruce Fischl wrote: >> > Hi Francesca >> > >> > why is the nifti 5-dimensional? The code is complaining that it doesn't >> > know how to intepret the input volume >> > >> > cheers >> > Bruce >> > On Sun, 30 Jul 2017, Francesca >> > Strappini wrote: >> > >> >> Hi, I'm trying to register to the surface a t-test map created with >> afni >> >> (3dttest++) but I got this error message: >> >> >> >> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage >> --surf-fwhm 3 >> >> --hemi lh --o movierestTest_lh.nii.gz >> >> >> >> srcvol = movierestTest.nii.gz >> >> srcreg unspecified >> >> srcregold = 0 >> >> srcwarp unspecified >> >> surf = white >> >> hemi = lh >> >> reshape = 0 >> >> interp = nearest >> >> float2int = round >> >> GetProjMax = 0 >> >> INFO: float2int code = 0 >> >> niiRead(): 5 dimensions in/media/francesca/DATA/Shared >> /fmri-experiments/fc_categories/searchlight/tes >> >> rest/movierestTest.nii.gz; unsupported >> >> Invalid argument >> >> ERROR: could not read movierestTest.nii.gz as type 24 >> >> >> >> Thanks >> >> Francesca >> >> >> >> >> >> -- >> >> Francesca Strappini, Ph.D. >> >> Neurobiology Department >> >> Weizmann Institute of Science >> >> 234 Herzl Street, Rehovot 7610001 Israel >> >> Tel.: +972 58 444 2584 <+972%2058-444-2584> >> >> E-mail: francesca.strapp...@weizmann.ac.il >> >> >> >> >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 <+972%2058-444-2584> > E-mail: francesca.strapp...@weizmann.ac.il > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] niiRead error
Thanks for the reply. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. I opened it with fslview and it looks like a normal 3-dimentional file. Thanks Francesca 2017-07-31 16:38 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > what version of FS are you running? > > > On 7/30/17 12:37 PM, Bruce Fischl wrote: > > Hi Francesca > > > > why is the nifti 5-dimensional? The code is complaining that it doesn't > > know how to intepret the input volume > > > > cheers > > Bruce > > On Sun, 30 Jul 2017, Francesca > > Strappini wrote: > > > >> Hi, I'm trying to register to the surface a t-test map created with afni > >> (3dttest++) but I got this error message: > >> > >> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage > --surf-fwhm 3 > >> --hemi lh --o movierestTest_lh.nii.gz > >> > >> srcvol = movierestTest.nii.gz > >> srcreg unspecified > >> srcregold = 0 > >> srcwarp unspecified > >> surf = white > >> hemi = lh > >> reshape = 0 > >> interp = nearest > >> float2int = round > >> GetProjMax = 0 > >> INFO: float2int code = 0 > >> niiRead(): 5 dimensions in/media/francesca/DATA/ > Shared/fmri-experiments/fc_categories/searchlight/tes > >> rest/movierestTest.nii.gz; unsupported > >> Invalid argument > >> ERROR: could not read movierestTest.nii.gz as type 24 > >> > >> Thanks > >> Francesca > >> > >> > >> -- > >> Francesca Strappini, Ph.D. > >> Neurobiology Department > >> Weizmann Institute of Science > >> 234 Herzl Street, Rehovot 7610001 Israel > >> Tel.: +972 58 444 2584 > >> E-mail: francesca.strapp...@weizmann.ac.il > >> > >> > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] niiRead error
Hi, I'm trying to register to the surface a *t*-test map created with afni (3dttest++) but I got this error message: mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage --surf-fwhm 3 --hemi lh --o movierestTest_lh.nii.gz srcvol = movierestTest.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 niiRead(): 5 dimensions in /media/francesca/DATA/Shared/fmri-experiments/fc_categories/searchlight/tesrest/movierestTest.nii.gz; unsupported Invalid argument ERROR: could not read movierestTest.nii.gz as type 24 Thanks Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] V3A ROI?
Wang, Mruczek, Arcaro, Kastner (2014). Probabilistic Maps of Visual Topography in Human Cortex. Cerebral Cortex, Oct;25(10):3911-31 2016-07-11 12:13 GMT+02:00 Anders Hougaard <ahouga...@dadlnet.dk>: > Dear experts, > > I am trying to find a probabilistic map of the visual cortical area V3A. > I have not been able to find this particular area in the standard atlases > in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but > not V3A. > Do any of you know have this ROI as a file or do you know of an atlas > which contains it? > An estimation based on an experiment, e.g. an average from retinotopic > maps of healthy subjects would also be very helpful. > > All the best, > Anders > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] retinotopic analysis
Hello Freesurfers, Where can I find any documentation about how is retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] retinotopy analysis documentation
Hello Freesurfers, I'm re-posting this question. Where can I find any documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg3-sess error
Thank you, I'll try! Best Francesca On Wednesday, June 15, 2016, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Sorry for the delay. Do you have polar angle data? Unfortunately, FSFAST > needs both. If you don't have polar, just copy the eccen data and call > it polar. for what you want to do it won't make much difference. > > On 06/08/2016 09:55 AM, Francesca Strappini wrote: > > I have only something similar in the temporal dynamics to the > > eccentricity data. I attached the Xtmp.mat file. > > Thank you! > > > > Francesca > > > > 2016-06-08 15:44 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu > <javascript:;> > > <mailto:gr...@nmr.mgh.harvard.edu <javascript:;>>>: > > > > Do you have both polar and eccen data? If so, can you send the > > Xtmp.mat file? > > > > > > On 6/8/16 6:08 AM, Francesca Strappini wrote: > >> Hi Freesurfer experts, > >> > >> I'm re-posting this message because I think it got lost. > >> > >> I'm trying to analyze some phase-encoded data with the eccentricity > >> protocol for retinotopic data and I'm having troubles with > >> selxavg3-sess. > >> > >> I run the following commands: > >> > >> mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj > >> lh -TR 2 > >> -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd > >> bold > >> > >> selxavg3-sess -a OrderDisorder.idsubj.lh -s > >> idsubj_OrderDisorder_continous > >> > >> and I got this error message: > >> > >> Found 122573/130829 (93.7) voxels in mask > >> Creating Design Matrix > >> ... creation time = 0.019 sec > >> DoMCFit = 1 > >> ntptot = 875, nX = 80, DOF = 795 > >> Saving X matrix to > >> > > /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat > >> Error using svd > >> Input to SVD must not contain NaN or Inf. > >> > >> Error in cond (line 35) > >> s = svd(A); > >> > >> Error in fast_selxavg3 (line 279) > >> XCond = cond(XtX); > >> > >> Thanks! > >> Best > >> Francesca > >> > >> > >> > >> -- > >> Francesca Strappini, Ph.D. > >> Neurobiology Department > >> Weizmann Institute of Science > >> 234 Herzl Street, Rehovot 7610001 Israel > >> Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584> > >> E-mail: francesca.strapp...@weizmann.ac.il <javascript:;> > >> <mailto:francesca.strapp...@weizmann.ac.il <javascript:;>> > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <javascript:;> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <javascript:;>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <javascript:;> Freesurfer@nmr.mgh.harvard.edu <javascript:;>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il <javascript:;> > > <mailto:francesca.strapp...@weizmann.ac.il <javascript:;>> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > > https://mail.nmr.mg
Re: [Freesurfer] selxavg3-sess error
Hi Doug, it looks like my email with attached the Xtmp.mat file didn't arrive. How can I send it to you? Thanks! Francesca 2016-06-08 15:44 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > Do you have both polar and eccen data? If so, can you send the Xtmp.mat > file? > > > On 6/8/16 6:08 AM, Francesca Strappini wrote: > > Hi Freesurfer experts, > > I'm re-posting this message because I think it got lost. > > I'm trying to analyze some phase-encoded data with the eccentricity > protocol for retinotopic data and I'm having troubles with selxavg3-sess. > > I run the following commands: > > mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 > -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold > > selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous > > and I got this error message: > > Found 122573/130829 (93.7) voxels in mask > Creating Design Matrix > ... creation time = 0.019 sec > DoMCFit = 1 > ntptot = 875, nX = 80, DOF = 795 > Saving X matrix to > > /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 35) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > Thanks! > Best > Francesca > > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] selxavg3-sess error
Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous and I got this error message: Found 122573/130829 (93.7) voxels in mask Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 875, nX = 80, DOF = 795 Saving X matrix to /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] selxavg3-sess error with phase-encoded data
Hi Freesurfer experts, I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous and I got this error message: Found 122573/130829 (93.7) voxels in mask Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 875, nX = 80, DOF = 795 Saving X matrix to /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); I attached the Xtmp.mat file from the output folder in case is needed. Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il Xtmp.mat Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface-based spatial smoothing model
Thank you! 2016-05-04 21:09 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > you can reference this one > http://www.ncbi.nlm.nih.gov/pubmed/17011792 > > > Smoothing and cluster thresholding for cortical surface-based group > analysis of fMRI data. > > Hagler DJ Jr > < > http://www.ncbi.nlm.nih.gov/pubmed/?term=Hagler%20DJ%20Jr%5BAuthor%5D=true_uid=17011792 > >^1 > , Saygin AP > < > http://www.ncbi.nlm.nih.gov/pubmed/?term=Saygin%20AP%5BAuthor%5D=true_uid=17011792 > >, > Sereno MI > < > http://www.ncbi.nlm.nih.gov/pubmed/?term=Sereno%20MI%5BAuthor%5D=true_uid=17011792 > >. > > > > On 05/03/2016 09:03 AM, Francesca Strappini wrote: > > Thank you! > > Is there a paper I can read as a reference? > > > > 2016-05-03 15:53 GMT+03:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu>>: > > > > Hi Francesca > > > > what's the difference? They are both approximations of Gaussians > > on the > > surface. We use iterative averaging which is a numerical > > approximation of > > a surface-based Gaussian. > > > > cheers > > Bruce > > > > > > On Tue, 3 May 2016, Francesca Strappini wrote: > > > > > Hi all, > > > > > > I would like to know which model has been implemented for the > > surface-based > > > spatial smoothing in Freesurfer (for example in mri_vol2surf). > > Heat kernel > > > smoothing and/or diffusion smoothing? > > > > > > Thank you > > > Best > > > > > > Francesca > > > > > > -- > > > Francesca Strappini, Ph.D. > > > Neurobiology Department > > > Weizmann Institute of Science > > > 234 Herzl Street, Rehovot 7610001 Israel > > > Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584> > > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface-based spatial smoothing model
Thank you! Is there a paper I can read as a reference? 2016-05-03 15:53 GMT+03:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Francesca > > what's the difference? They are both approximations of Gaussians on the > surface. We use iterative averaging which is a numerical approximation of > a surface-based Gaussian. > > cheers > Bruce > > > On Tue, 3 May 2016, Francesca Strappini wrote: > > > Hi all, > > > > I would like to know which model has been implemented for the > surface-based > > spatial smoothing in Freesurfer (for example in mri_vol2surf). Heat > kernel > > smoothing and/or diffusion smoothing? > > > > Thank you > > Best > > > > Francesca > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] surface-based spatial smoothing model
Hi all, I would like to know which model has been implemented for the surface-based spatial smoothing in Freesurfer (for example in mri_vol2surf). Heat kernel smoothing and/or diffusion smoothing? Thank you Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2surf misaligment
Dear Freesurfers, I run the preprocessing step of some functional data with preproc-sess, then the Fourier analysis with matlab. Now, I'm trying to plot this data on the surface: mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz I used as registration matrix the one produced by the preprocessing step but when I try to visualize the map on the surface it looks like completely misaligned. Thank you Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] converting labels to MNI space
Thank you! I run the recon-all on the MNI brain and now the first step, label2label, produced a label which is perfectly mapped on the surface of the MNI template. I tried to run the second step, mapping the new label to the volume, but I still got the shift downward. mri_label2vol --label lh.V1dorsalLG_MNI.label --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz --identity Best Francesca 2015-12-01 20:26 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > Try adding --invertmtx to the mri_label2vol command. I don't think the > label2label command does anything, does it? Also, you might have better > alignment if you run recon-all on the mni152 brain, then use > mri_label2label to map the label from the individual into the 152 space > using the surface transform, then convert that to the volume. > > On 11/30/2015 10:13 AM, Francesca Strappini wrote: > > Dear FreeSurfer experts, > > > > I'm trying to convert some retinotopic labels I created on the surface > > of each individual subject to MNI305 space for FSL. > > > > I run the following commands, but the output is not registered > > correctly. It seems to be shifted downward. > > > > mni152reg --s LG > > > > mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod > > surface --trglabel lh.V1dorsalLG_new.label --hemi lh > > > > mri_label2vol --label lh.V1dorsalLG_new.label --reg > > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp > > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > > lh.V1dorsalLG_new_MNI.nii.gz > > > > Thanks for your help, > > Francesca > > > > -- > > Francesca Strappini, Ph.D. > > Neurobiology Department > > Weizmann Institute of Science > > 234 Herzl Street, Rehovot 7610001 Israel > > Tel.: +972 58 444 2584 > > E-mail: francesca.strapp...@weizmann.ac.il > > <mailto:francesca.strapp...@weizmann.ac.il> > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] converting labels to MNI space
Thanks! I run this command: mri_label2vol --label lh.V1dorsalLG_MNI.label --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz but unfortunately, it gave me the same big downward shift (I checked it with fslview). But if I try to open the ROI with freeview it gives me this error: freeview.bin: empty label LabelRead failed freeview.bin: empty label 2015-12-03 16:57 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz instead > of --identity > > > > On 12/3/15 8:46 AM, Francesca Strappini wrote: > > Thank you! > > I run the recon-all on the MNI brain and now the first step, label2label, > produced a label which is perfectly mapped on the surface of the MNI > template. > I tried to run the second step, mapping the new label to the volume, but I > still got the shift downward. > > mri_label2vol --label lh.V1dorsalLG_MNI.label --temp > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > lh.V1dorsalLG_MNI.nii.gz --identity > > Best > Francesca > > > > 2015-12-01 20:26 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> Try adding --invertmtx to the mri_label2vol command. I don't think the >> label2label command does anything, does it? Also, you might have better >> alignment if you run recon-all on the mni152 brain, then use >> mri_label2label to map the label from the individual into the 152 space >> using the surface transform, then convert that to the volume. >> >> On 11/30/2015 10:13 AM, Francesca Strappini wrote: >> > Dear FreeSurfer experts, >> > >> > I'm trying to convert some retinotopic labels I created on the surface >> > of each individual subject to MNI305 space for FSL. >> > >> > I run the following commands, but the output is not registered >> > correctly. It seems to be shifted downward. >> > >> > mni152reg --s LG >> > >> > mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod >> > surface --trglabel lh.V1dorsalLG_new.label --hemi lh >> > >> > mri_label2vol --label lh.V1dorsalLG_new.label --reg >> > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp >> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o >> > lh.V1dorsalLG_new_MNI.nii.gz >> > >> > Thanks for your help, >> > Francesca >> > >> > -- >> > Francesca Strappini, Ph.D. >> > Neurobiology Department >> > Weizmann Institute of Science >> > 234 Herzl Street, Rehovot 7610001 Israel >> > Tel.: +972 58 444 2584 >> > E-mail: francesca.strapp...@weizmann.ac.il >> > <mailto:francesca.strapp...@weizmann.ac.il> >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer ma
Re: [Freesurfer] converting labels to MNI space
Thank you Doug and Bruce now everything works and the region is perfectly aligned! Best Francesca 2015-12-03 18:03 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > oops, gave you the wrong option, it should be > > --regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz > > > > On 12/03/2015 10:22 AM, Francesca Strappini wrote: > > Thanks! > > > > I run this command: > > > > mri_label2vol --label lh.V1dorsalLG_MNI.label --temp > > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader > > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > > lh.V1dorsalLG_MNI.nii.gz > > > > but unfortunately, it gave me the same big downward shift (I checked > > it with fslview). > > > > But if I try to open the ROI with freeview it gives me this error: > > freeview.bin: empty label > > LabelRead failed > > freeview.bin: empty label > > > > 2015-12-03 16:57 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>: > > > > Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz > > instead of --identity > > > > > > > > On 12/3/15 8:46 AM, Francesca Strappini wrote: > >> Thank you! > >> > >> I run the recon-all on the MNI brain and now the first step, > >> label2label, produced a label which is perfectly mapped on the > >> surface of the MNI template. > >> I tried to run the second step, mapping the new label to the > >> volume, but I still got the shift downward. > >> > >> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp > >> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > >> lh.V1dorsalLG_MNI.nii.gz --identity > >> > >> Best > >> Francesca > >> > >> > >> > >> 2015-12-01 20:26 GMT+02:00 Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>: > >> > >> Try adding --invertmtx to the mri_label2vol command. I don't > >> think the > >> label2label command does anything, does it? Also, you might > >> have better > >> alignment if you run recon-all on the mni152 brain, then use > >> mri_label2label to map the label from the individual into the > >> 152 space > >> using the surface transform, then convert that to the volume. > >> > >> On 11/30/2015 10:13 AM, Francesca Strappini wrote: > >> > Dear FreeSurfer experts, > >> > > >> > I'm trying to convert some retinotopic labels I created on > >> the surface > >> > of each individual subject to MNI305 space for FSL. > >> > > >> > I run the following commands, but the output is not registered > >> > correctly. It seems to be shifted downward. > >> > > >> > mni152reg --s LG > >> > > >> > mri_label2label --srclabel lh.V1dorsalLG.label --s LG > >> --regmethod > >> > surface --trglabel lh.V1dorsalLG_new.label --hemi lh > >> > > >> > mri_label2vol --label lh.V1dorsalLG_new.label --reg > >> > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg > >> --temp > >> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o > >> > lh.V1dorsalLG_new_MNI.nii.gz > >> > > >> > Thanks for your help, > >> > Francesca > >> > > >> > -- > >> > Francesca Strappini, Ph.D. > >> > Neurobiology Department > >> > Weizmann Institute of Science > >> > 234 Herzl Street, Rehovot 7610001 Israel > >> > Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584> > >> > E-mail: francesca.strapp...@weizmann.ac.il > >> <mailto:francesca.strapp...@weizmann.ac.il> > >> > <mailto:francesca.strapp...@weizmann.ac.il > >> <mailto:francesca.strapp...@weizmann.ac.il>> > >> > > >> > > >> > ___ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.
[Freesurfer] converting labels to MNI space
Dear FreeSurfer experts, I'm trying to convert some retinotopic labels I created on the surface of each individual subject to MNI305 space for FSL. I run the following commands, but the output is not registered correctly. It seems to be shifted downward. mni152reg --s LG mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod surface --trglabel lh.V1dorsalLG_new.label --hemi lh mri_label2vol --label lh.V1dorsalLG_new.label --reg /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_new_MNI.nii.gz Thanks for your help, Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_convert gifti
Hi Ziad, yes, it's related to that. Thank you for the help! Best Francesca 2015-05-06 16:25 GMT+03:00 Ziad Saad sa...@mail.nih.gov: Hello folks, I am ccing all those on the thread because I am not sure my reply to the support list will get through. GIFTI is the way to go as Matt suggested and all of AFNI and SUMA programs support that format for datasets. The .dset itself is not a format, merely a convenient way to indicate that a file is a dataset (as opposed to a surface, tracts, etc.). The format of .dset can be .gii, .niml, or .1D which is the simple ascii table of numbers. Francesca: I suspect this is related to the AFNI message board posting from a couple of days ago. I have not gotten around to it yet but I hope to do so later today. cheers Ziad On May 5, 2015, at 18:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sorry, I think this may be a question for the SUMA people - I don't know what .dset format is. Are you going to do the masking within SUMA? I'll cc Ziad so he can chime in. cheers Bruce On Tue, 5 May 2015, Francesca Strappini wrote: I'm trying to mask a time series dataset that I mapped to the surface in SUMA (surface created with freesurfer and imported into SUMA). I think the input should be in the .dset fomat (region mapped to the surface). The problem is that when I save my label the annotation file has only a list of vertexes related to the region and not all the surface vertexes. Thanks for the help! Francesca 2015-05-05 23:04 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: you can just create a label file I guess. What input does SUMA take? On Tue, 5 May 2015, Francesca Strappini wrote: Sorry, just to be clear, I meant how can I create a mask on the surface in which at each vertex is assigned a value, 0 or 1. I need to create this mask for exporting the freesurfer labels into SUMA and ultimately to extract the time series from each vertex. Thanks Francesca 2015-05-05 16:06 GMT+03:00 Francesca Strappini francescastrapp...@gmail.com: Thank you! Do you know which function should I use? Best Francesca 2015-05-05 15:30 GMT+03:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: yes, you can use a label for this (we use the ?h.cortex.label for this purpose routinely to remove non-cortical stuff) On Tue, 5 May 2015, Francesca Strappini wrote: Thank you so much! I understand what's the problem and I will make my custom ctab file. Last question, about the annot files, is it possible with freesurfer to create a mask with the annot or the label files in which the value 1 is assigned to the region and 0 to the rest of the brain? Thanks again! Best Francesca 2015-05-05 4:20 GMT+03:00 Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu: Francesca, I looked at the files you sent and replicated the problem. It is due to creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the colortable file. You should create your own colortable file, which is simple to do, and create a new .annot file using that colortable (ie, the --ctab option in mris_label2annot). Here is a simple colortable.txt file (just a text file) with four entries, which in this example, means that you have three annotations. The first entry must be as it is shown, ie, 'unknown', as this is used to automatically 'label' all the vertices which do not have a .label
Re: [Freesurfer] mris_convert gifti
Hi Matt, I can answer only partially to your question. SUMA/afni in general supports GIFTI format but I don't know if is it possible to directly convert from GIFTI to .dset. Usually I convert my annot file to .niml.roi with FSread_annot and .niml.roi to .1D.dset with ROI2dataset. Best Francesca 2015-05-06 1:53 GMT+03:00 Matt Glasser m...@ma-tea.com: Does SUMA support GIFTI and provide a utility to convert between its formats and GIFTI? I was also wondering what a .dset was and how to get it into GIFTI so it could be easily used across software platforms. Thanks, Matt. On 5/5/15, 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sorry, I think this may be a question for the SUMA people - I don't know what .dset format is. Are you going to do the masking within SUMA? I'll cc Ziad so he can chime in. cheers Bruce On Tue, 5 May 2015, Francesca Strappini wrote: I'm trying to mask a time series dataset that I mapped to the surface in SUMA (surface created with freesurfer and imported into SUMA). I think the input should be in the .dset fomat (region mapped to the surface). The problem is that when I save my label the annotation file has only a list of vertexes related to the region and not all the surface vertexes. Thanks for the help! Francesca 2015-05-05 23:04 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: you can just create a label file I guess. What input does SUMA take? On Tue, 5 May 2015, Francesca Strappini wrote: Sorry, just to be clear, I meant how can I create a mask on the surface in which at each vertex is assigned a value, 0 or 1. I need to create this mask for exporting the freesurfer labels into SUMA and ultimately to extract the time series from each vertex. Thanks Francesca 2015-05-05 16:06 GMT+03:00 Francesca Strappini francescastrapp...@gmail.com: Thank you! Do you know which function should I use? Best Francesca 2015-05-05 15:30 GMT+03:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: yes, you can use a label for this (we use the ?h.cortex.label for this purpose routinely to remove non-cortical stuff) On Tue, 5 May 2015, Francesca Strappini wrote: Thank you so much! I understand what's the problem and I will make my custom ctab file. Last question, about the annot files, is it possible with freesurfer to create a mask with the annot or the label files in which the value 1 is assigned to the region and 0 to the rest of the brain? Thanks again! Best Francesca 2015-05-05 4:20 GMT+03:00 Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu: Francesca, I looked at the files you sent and replicated the problem. It is due to creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the colortable file. You should create your own colortable file, which is simple to do, and create a new .annot file using that colortable (ie, the --ctab option in mris_label2annot). Here is a simple colortable.txt file (just a text file) with four entries, which in this example, means that you have three annotations. The first entry must be as it is shown, ie, 'unknown', as this is used to automatically 'label' all the vertices which do not have a .label file. 0 unknown 25 5 250
Re: [Freesurfer] mris_convert gifti
Thank you so much! I understand what's the problem and I will make my custom ctab file. Last question, about the annot files, is it possible with freesurfer to create a mask with the annot or the label files in which the value 1 is assigned to the region and 0 to the rest of the brain? Thanks again! Best Francesca 2015-05-05 4:20 GMT+03:00 Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu: Francesca, I looked at the files you sent and replicated the problem. It is due to creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the colortable file. You should create your own colortable file, which is simple to do, and create a new .annot file using that colortable (ie, the --ctab option in mris_label2annot). Here is a simple colortable.txt file (just a text file) with four entries, which in this example, means that you have three annotations. The first entry must be as it is shown, ie, 'unknown', as this is used to automatically 'label' all the vertices which do not have a .label file. 0 unknown 25 5 250 1 mylabel1 0 92 230 2 mylabel2131 148 2550 3 mylabel3 0 0 2550 I fixed the code locally so that it doesn't segfault, and you can get the new mris_convert here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/bin/ but note this does not fix your core problem, it only allows mris_convert to run to completion and create a valid .annot.gii file. It will still have strange label names for your annotations (like Left_Hippocampus) taken from the embedded FreeSurferColorLUT. Nick On Thu, 2015-04-30 at 14:17 +0300, Francesca Strappini wrote: Hi, sorry to bother, I'm re-posting this question just in case it got lost. Thanks. Hi, I have a question about mris_convert. I've created some regions on the surface and now I would like to make them directly readable into SUMA. I ran this command but it ended with an error message. mris_convert --annot lh.EKppa.annot /usr/local/freesurfer/subjects/EK/surf/lh.white lh.EKppa.annot.gii reading colortable from annotation file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) Segmentation fault (core dumped) I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 running on Ubuntu 14.04.2 LTS. Thanks in advance for the help! Best Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_convert gifti
I'm trying to mask a time series dataset that I mapped to the surface in SUMA (surface created with freesurfer and imported into SUMA). I think the input should be in the .dset fomat (region mapped to the surface). The problem is that when I save my label the annotation file has only a list of vertexes related to the region and not all the surface vertexes. Thanks for the help! Francesca 2015-05-05 23:04 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: you can just create a label file I guess. What input does SUMA take? On Tue, 5 May 2015, Francesca Strappini wrote: Sorry, just to be clear, I meant how can I create a mask on the surface in which at each vertex is assigned a value, 0 or 1. I need to create this mask for exporting the freesurfer labels into SUMA and ultimately to extract the time series from each vertex. Thanks Francesca 2015-05-05 16:06 GMT+03:00 Francesca Strappini francescastrapp...@gmail.com: Thank you! Do you know which function should I use? Best Francesca 2015-05-05 15:30 GMT+03:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: yes, you can use a label for this (we use the ?h.cortex.label for this purpose routinely to remove non-cortical stuff) On Tue, 5 May 2015, Francesca Strappini wrote: Thank you so much! I understand what's the problem and I will make my custom ctab file. Last question, about the annot files, is it possible with freesurfer to create a mask with the annot or the label files in which the value 1 is assigned to the region and 0 to the rest of the brain? Thanks again! Best Francesca 2015-05-05 4:20 GMT+03:00 Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu: Francesca, I looked at the files you sent and replicated the problem. It is due to creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the colortable file. You should create your own colortable file, which is simple to do, and create a new .annot file using that colortable (ie, the --ctab option in mris_label2annot). Here is a simple colortable.txt file (just a text file) with four entries, which in this example, means that you have three annotations. The first entry must be as it is shown, ie, 'unknown', as this is used to automatically 'label' all the vertices which do not have a .label file. 0 unknown 25 5 250 1 mylabel1 0 92 230 2 mylabel2131 148 2550 3 mylabel3 0 0 2550 I fixed the code locally so that it doesn't segfault, and you can get the new mris_convert here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Lin ux-centos6_x86_64-stable-pub-v5.3.0/bin/ but note this does not fix your core problem, it only allows mris_convert to run to completion and create a valid .annot.gii file. It will still have strange label names for your annotations (like Left_Hippocampus) taken from the embedded FreeSurferColorLUT. Nick On Thu, 2015-04-30 at 14:17 +0300, Francesca Strappini wrote: Hi, sorry to bother, I'm re-posting this question just in case it got lost. Thanks. Hi, I have a question about mris_convert. I've created some regions on the surface and now I would like to make them directly readable into SUMA. I ran this command but it ended with an error message. mris_convert --annot lh.EKppa.annot /usr/local/freesurfer/subjects/EK/surf/lh.white lh.EKppa.annot.gii reading colortable from annotation file... colortable with 14176 entries read (originally
[Freesurfer] mris_convert gifti
Hi, sorry to bother, I'm re-posting this question just in case it got lost. Thanks. Hi, I have a question about mris_convert. I've created some regions on the surface and now I would like to make them directly readable into SUMA. I ran this command but it ended with an error message. mris_convert --annot lh.EKppa.annot /usr/local/freesurfer/subjects/EK/surf/lh.white lh.EKppa.annot.gii reading colortable from annotation file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) Segmentation fault (core dumped) I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 running on Ubuntu 14.04.2 LTS. Thanks in advance for the help! Best Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_convert converting annot to gifti format
Hi, I have a question about mris_convert. I've created some regions on the surface and now I would like to make them directly readable into SUMA. I ran this command but it ended with an error message. mris_convert --annot lh.EKppa.annot /usr/local/freesurfer/subjects/EK/surf/lh.white lh.EKppa.annot.gii reading colortable from annotation file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) Segmentation fault (core dumped) I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 running on Ubuntu 14.04.2 LTS. Thanks in advance for the help! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_pmake update
Dear Freesurfer experts, I'm currently working with Freesurfer 5.3-stable and I would like to calculate the geodesic distance between two points. I red in the support main-list that in this Freesurfer's version 'mris_pmake' might be outdated. How can I get the updated version? Thanks Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_pmake update
Thank you! I have Ubuntu 14.04.1 LTS, 64 bit. Best Francesca 2015-01-08 16:45 GMT+02:00 Rudolph Pienaar rudolph@gmail.com: I can send you the updated binary. What Linux are you running on? CentOS? 32 bit? 64 bit? Best -=R On 1/8/15 09:23 , Francesca Strappini wrote: Dear Freesurfer experts, I'm currently working with Freesurfer 5.3-stable and I would like to calculate the geodesic distance between two points. I red in the support main-list that in this Freesurfer's version 'mris_pmake' might be outdated. How can I get the updated version? Thanks Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il mailto:francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error with fast_selxavg3
Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and 2 of eccentricity. Francesca On Monday, November 10, 2014, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: There are a bunch of columns in the design matrix that are 0, meaning that it expects some kind of stimulus to be there but it was not in the parfile. Do you only have eccen for this or do you also have polar? doug On 11/08/2014 11:25 AM, Francesca Strappini wrote: Hi, I attached the file, thank you! Best Francesca 2014-11-06 18:58 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu javascript:; mailto:gr...@nmr.mgh.harvard.edu javascript:;: Can you send me /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat On 11/06/2014 09:53 AM, Francesca Strappini wrote: Dear all, I'm trying to run a retinotopy analysis in several subjects but it crashed with an error in one subject. I ran this command line: selxavg3-sess -a rtopy.HS.rh -s SUBJ09 and this is the last part of the output with the error message. Any help would be much appreciated. Best Francesca M A T L A B (R) Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 Your MATLAB license will expire in 56 days. Please contact your system administrator or MathWorks to renew this license. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com http://www.mathworks.com. sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s SUBJ09 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# SUBJ09 ### /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed Extension format = nii.gz nruns = 4 autostimdur = outanadir = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh Found 110059/126364 (87.1) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 960, nX = 36, DOF = 924 Saving X matrix to /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il javascript:; mailto:francesca.strapp...@weizmann.ac.il javascript:; mailto:francesca.strapp...@weizmann.ac.il javascript:; mailto:francesca.strapp...@weizmann.ac.il javascript:; ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; mailto:Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu javascript:; mailto: gr...@nmr.mgh.harvard.edu javascript:; Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; mailto: Freesurfer
[Freesurfer] error with fast_selxavg3
Dear all, I'm trying to run a retinotopy analysis in several subjects but it crashed with an error in one subject. I ran this command line: selxavg3-sess -a rtopy.HS.rh -s SUBJ09 and this is the last part of the output with the error message. Any help would be much appreciated. Best Francesca M A T L A B (R) Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 Your MATLAB license will expire in 56 days. Please contact your system administrator or MathWorks to renew this license. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s SUBJ09 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# SUBJ09 ### /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed Extension format = nii.gz nruns = 4 autostimdur = outanadir = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh Found 110059/126364 (87.1) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 960, nX = 36, DOF = 924 Saving X matrix to /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg3-sess error
Thank you, now it works! Best Francesca 2014-09-08 15:24 GMT+03:00 Douglas Greve gr...@nmr.mgh.harvard.edu: It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001 does that file exist? Have you run preproc-sess? doug On 8/28/14 9:49 AM, Francesca Strappini wrote: Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh -- selxavg3-sess logfile is /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log -- --- /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 Thu Aug 28 16:33:53 IDT 2014 anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output No window system found. Java option 'MWT' ignored. Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. M A T L A B (R) Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopy sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# SUBJ01 ### /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy Extension format = nii.gz ERROR: cannot determine format of /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 ERROR: attempting to read /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 -- ERROR: fast_selxavg3() failed\n ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fieldsign map display
Yes, this was the command line fieldsign-sess -a rtopy.LG.lh -s SUBJ02 -patch lh.full.flat.patch.3d -fwhm 0 Thanks! Francesca 2014-09-04 15:52 GMT+03:00 SHAHIN NASR sha...@nmr.mgh.harvard.edu: Hi, Have you ran fieldsign-sess after your selxavg3-sess? On Thu, Sep 4, 2014 at 8:35 AM, Francesca Strappini francescastrapp...@gmail.com wrote: Dear all, I'm trying to display the fieldsign map. I used standard rotating-wedge and expanding-ring paradigm, and I followed the steps described in FsFastIndividualRetinotopy Analysis. I'm running freesurfer on Ubuntu 14.04. Polar angle and eccentricity map look good but I can't properly display the fieldsign map as an alternation of two colours. I attached a screen-shot as example. Any suggestion? Thanks for the help! Francesca The command line is; tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign and that's the output: shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy tksurfer-sess -a rtopy.DM.lh -s SUBJ01 -fieldsign Surface DM lh Map Surface DM lh $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $ Linux shalim-ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 2 17:28:57 IDT 2014 /usr/local/freesurfer/bin/tksurfer list fieldsign con/map fieldsign /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz maplist /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz mri_concat /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fieldsign.nii.gz --o /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii cd /usr/local/freesurfer/fsfast/MeytalRetinotopy setenv SUBJECTS_DIR /usr/local/freesurfer/subjects tksurfer DM lh inflated -overlay /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 0.5 -fmid 2.2500 -fslope .28571428571428571428 -mask /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz -mask-thresh 0.5 -fthresh .01 Contrasts 0 fieldsign setting colscalebarflag to 1 setting fthresh to 0.5000 setting fmid to 2.2500 setting fslope to 0.2857 mrismaskfile /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz... setting mrismaskthresh to 0.5000 setting fthresh to 0.0100 subject is DM hemiis lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/fsfast/MeytalRetinotopy checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/DM) Reading /usr/local/freesurfer/subjects/DM/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/DM/mri/orig.mgz surfer: vertices=118099, faces=236194 tkmedit: Trying to open /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.dat surfer: Interpreting overlay volume /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/tksconcat.nii as encoded scalar volume. surfer: curvature read: min=-1.094241 max=1.337460 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 8089 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(DM) Reading mris mask /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh/fieldsign/fsig.nii.gz surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ^CKilled Area degli allegati Visualizza anteprima allegato fieldsign_map.tiff Fai clic qui per rispondere o inoltrare il messaggio 7,02 GB (46%) di 15 GB utilizzati Gestisci Ultima attività dell'account: 2 minuti fa Dettagli ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
[Freesurfer] selxavg3-sess error
Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh -- selxavg3-sess logfile is /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log -- --- /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 Thu Aug 28 16:33:53 IDT 2014 anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output No window system found. Java option 'MWT' ignored. Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. M A T L A B (R) Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopy sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# SUBJ01 ### /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy Extension format = nii.gz ERROR: cannot determine format of /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 ERROR: attempting to read /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 -- ERROR: fast_selxavg3() failed\n ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coomand not found
Hi, thanks for the help! These are the outputs: 1) What is the output of the following: ls -ld $FREESURFER_HOME/bin drwxrwxrwx 1 francesca francesca 118784 May 14 2013 /media/Shared_Data/freesurfer/bin 2) After sourcing FreeSurfer, what happens when you type: tkmedit -f $SUBJECTS_DIR/sample-001.mgz shalim-ubunut:/media/Shared_Data/freesurfer tkmedit -f $SUBJECTS_DIR/sample-001.mgz /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit -f $SUBJECTS_DIR/sample-001.mgz [sudo] password for francesca: sudo: tkmedit: command not found 3) Does freeview open (just type 'freeview' after sourcing FreeSurfer)? shalim-ubunut:/media/Shared_Data/freesurfer freeview /media/Shared_Data/freesurfer/bin/freeview: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo freeview sudo: freeview: command not found Francesca Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni shalim-ubunut:/media/Shared_Data/freesurfer pwd /media/Shared_Data/freesurfer shalim-ubunut:/media/Shared_Data/freesurfer tkmedit bert orig.mgz /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit bert orig.mgz sudo: tkmedit: command not found shalim-ubunut:/media/Shared_Data/freesurfer/bin ls -la tkmedit -rwxrwxrwx 1 francesca francesca 102 May 14 2013 tkmedit 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Ok, could you send the entire terminal output? Thanks. -Louis On Mon, 12 May 2014, Francesca Strappini wrote: Thanks Louis! Yes, I did run tkmedit from the same terminal window I have sourced freesurfer... Francesca 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automatically when opening a new terminal or setting up an alias to make the process quicker. -Louis On Sat, 10 May 2014, Francesca Strappini wrote: Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail
Re: [Freesurfer] Coomand not found
Ok, thank you! I sourced freesurfer and then I tried: cd $FREESURFER_HOME sudo chmod -R a+rX * But I still get the same error: shalim-ubunut:/media/Shared_Data/freesurfer freeview /media/Shared_Data/freesurfer/bin/freeview: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo freeview sudo: freeview: command not found Best Francesca 2014-05-14 16:35 GMT+03:00 Martin Reuter mreu...@nmr.mgh.harvard.edu: Hi Francesca, you need to make sure that the current user has read and execute permissions of the Freesurfer files. Either make sure that the FreeSurfer directory is in the same group as the user and give group rights, or give read and execute rights to everyone. source freesurfer first cd $FREESURFER_HOME sudo chmod -R g+rX * for setting group rights, assuming the group is the same, you can also change the group via: sudo chgrp -R groupname * where groupname is the new group. If you want to give world read/execute permissions do this: cd $FREESURFER_HOME sudo chmod -R a+rX * Best, Martin On 05/14/2014 04:16 AM, Francesca Strappini wrote: Hi, thanks for the help! These are the outputs: 1) What is the output of the following: ls -ld $FREESURFER_HOME/bin drwxrwxrwx 1 francesca francesca 118784 May 14 2013 /media/Shared_Data/freesurfer/bin 2) After sourcing FreeSurfer, what happens when you type: tkmedit -f $SUBJECTS_DIR/sample-001.mgz shalim-ubunut:/media/Shared_Data/freesurfer tkmedit -f $SUBJECTS_DIR/sample-001.mgz /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit -f $SUBJECTS_DIR/sample-001.mgz [sudo] password for francesca: sudo: tkmedit: command not found 3) Does freeview open (just type 'freeview' after sourcing FreeSurfer)? shalim-ubunut:/media/Shared_Data/freesurfer freeview /media/Shared_Data/freesurfer/bin/freeview: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo freeview sudo: freeview: command not found Francesca Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni shalim-ubunut:/media/Shared_Data/freesurfer pwd /media/Shared_Data/freesurfer shalim-ubunut:/media/Shared_Data/freesurfer tkmedit bert orig.mgz /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit bert orig.mgz sudo: tkmedit: command not found shalim-ubunut:/media/Shared_Data/freesurfer/bin ls -la tkmedit -rwxrwxrwx 1 francesca francesca 102 May 14 2013 tkmedit 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Ok, could you send the entire terminal output? Thanks. -Louis On Mon, 12 May 2014, Francesca Strappini wrote: Thanks Louis! Yes, I did run tkmedit from the same terminal window I have sourced freesurfer... Francesca 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automatically when opening a new terminal or setting up an alias to make the process quicker. -Louis On Sat, 10 May 2014, Francesca Strappini wrote: Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains
Re: [Freesurfer] Coomand not found
Yes, it's a dual boot system (Windows7 and Ubuntu 12.04 LTS)
I'm running FreeSurfer on Ubuntu.
Shared_Data is shared between Windows and Ubuntu.
I can try to install FreeSurfer on Linux /usr/local if you think that this
can help.
Thanks!
Francesca
2014-05-14 17:09 GMT+03:00 dgw dgwake...@gmail.com:
Francesca,
Is this a dual boot system (do you have multiple operating systems
installed on it)?
Are you running FreeSurfer in a virtual machine?
It sounds like another operating system may be controlling the
permissions of the /media/Shared_Data directory.
D
On Wed, May 14, 2014 at 9:51 AM, Francesca Strappini
francescastrapp...@gmail.com wrote:
Ok, thank you!
I sourced freesurfer and then I tried:
cd $FREESURFER_HOME
sudo chmod -R a+rX *
But I still get the same error:
shalim-ubunut:/media/Shared_Data/freesurfer freeview
/media/Shared_Data/freesurfer/bin/freeview: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer sudo freeview
sudo: freeview: command not found
Best
Francesca
2014-05-14 16:35 GMT+03:00 Martin Reuter mreu...@nmr.mgh.harvard.edu:
Hi Francesca,
you need to make sure that the current user has read and execute
permissions of the Freesurfer files. Either make sure that the
FreeSurfer
directory is in the same group as the user and give group rights, or
give
read and execute rights to everyone.
source freesurfer first
cd $FREESURFER_HOME
sudo chmod -R g+rX *
for setting group rights, assuming the group is the same, you can also
change the group via:
sudo chgrp -R groupname *
where groupname is the new group.
If you want to give world read/execute permissions do this:
cd $FREESURFER_HOME
sudo chmod -R a+rX *
Best, Martin
On 05/14/2014 04:16 AM, Francesca Strappini wrote:
Hi, thanks for the help!
These are the outputs:
1) What is the output of the following:
ls -ld $FREESURFER_HOME/bin
drwxrwxrwx 1 francesca francesca 118784 May 14 2013
/media/Shared_Data/freesurfer/bin
2) After sourcing FreeSurfer, what happens when you type:
tkmedit -f $SUBJECTS_DIR/sample-001.mgz
shalim-ubunut:/media/Shared_Data/freesurfer tkmedit -f
$SUBJECTS_DIR/sample-001.mgz
/media/Shared_Data/freesurfer/bin/tkmedit: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit -f
$SUBJECTS_DIR/sample-001.mgz
[sudo] password for francesca:
sudo: tkmedit: command not found
3) Does freeview open (just type 'freeview' after sourcing
FreeSurfer)?
shalim-ubunut:/media/Shared_Data/freesurfer freeview
/media/Shared_Data/freesurfer/bin/freeview: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer sudo freeview
sudo: freeview: command not found
Francesca
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /media/Shared_Data/freesurfer
FSFAST_HOME /media/Shared_Data/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects
MNI_DIR /media/Shared_Data/freesurfer/mni
shalim-ubunut:/media/Shared_Data/freesurfer pwd
/media/Shared_Data/freesurfer
shalim-ubunut:/media/Shared_Data/freesurfer tkmedit bert orig.mgz
/media/Shared_Data/freesurfer/bin/tkmedit: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit bert
orig.mgz
sudo: tkmedit: command not found
shalim-ubunut:/media/Shared_Data/freesurfer/bin ls -la tkmedit
-rwxrwxrwx 1 francesca francesca 102 May 14 2013 tkmedit
2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke
vi...@nmr.mgh.harvard.edu:
Ok, could you send the entire terminal output?
Thanks.
-Louis
On Mon, 12 May 2014, Francesca Strappini wrote:
Thanks Louis!
Yes, I did run tkmedit from the same terminal window I have sourced
freesurfer...
Francesca
2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke
vi...@nmr.mgh.harvard.edu:
Hi Francesca,
Are you trying to run the tkmedit command in the same terminal
window you
have sourced freesurfer? You'll need to source freesurfer in any
new
terminal window you open before being able to run any freesurfer
commands.
It's possible to set it up so that freesurfer is sourced
automatically
when opening a new terminal or setting up an alias to make the
process
quicker.
-Louis
On Sat, 10 May 2014, Francesca Strappini wrote:
Hi, I'm just starting out with freesurfer. I downloaded
CentOS6_x86_64
and I have Ubuntu 12.04 LTS. I have set up the licence file and
configured freesurfer:
tcsh
setenv FREESURFER_HOME /media/Shared_Data/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /media/Shared_Data/freesurfer
FSFAST_HOME /media
Re: [Freesurfer] Coomand not found
ok, thank you! Francesca On Wednesday, May 14, 2014, dgw dgwake...@gmail.com wrote: It doesn't need to be in /usr/local (I'm not sure if the FreeSurfer team has a preferred install location), but it is probably simpler (read: there may be some complex way to get it to work on a shared directory, but it would take a lot of digging to figure out how) to install it on the pure linux partition. HTH, D On Wed, May 14, 2014 at 10:18 AM, Francesca Strappini francescastrapp...@gmail.com wrote: Yes, it's a dual boot system (Windows7 and Ubuntu 12.04 LTS) I'm running FreeSurfer on Ubuntu. Shared_Data is shared between Windows and Ubuntu. I can try to install FreeSurfer on Linux /usr/local if you think that this can help. Thanks! Francesca 2014-05-14 17:09 GMT+03:00 dgw dgwake...@gmail.com: Francesca, Is this a dual boot system (do you have multiple operating systems installed on it)? Are you running FreeSurfer in a virtual machine? It sounds like another operating system may be controlling the permissions of the /media/Shared_Data directory. D On Wed, May 14, 2014 at 9:51 AM, Francesca Strappini francescastrapp...@gmail.com wrote: Ok, thank you! I sourced freesurfer and then I tried: cd $FREESURFER_HOME sudo chmod -R a+rX * But I still get the same error: shalim-ubunut:/media/Shared_Data/freesurfer freeview /media/Shared_Data/freesurfer/bin/freeview: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo freeview sudo: freeview: command not found Best Francesca 2014-05-14 16:35 GMT+03:00 Martin Reuter mreu...@nmr.mgh.harvard.edu : Hi Francesca, you need to make sure that the current user has read and execute permissions of the Freesurfer files. Either make sure that the FreeSurfer directory is in the same group as the user and give group rights, or give read and execute rights to everyone. source freesurfer first cd $FREESURFER_HOME sudo chmod -R g+rX * for setting group rights, assuming the group is the same, you can also change the group via: sudo chgrp -R groupname * where groupname is the new group. If you want to give world read/execute permissions do this: cd $FREESURFER_HOME sudo chmod -R a+rX * Best, Martin On 05/14/2014 04:16 AM, Francesca Strappini wrote: Hi, thanks for the help! These are the outputs: 1) What is the output of the following: ls -ld $FREESURFER_HOME/bin drwxrwxrwx 1 francesca francesca 118784 May 14 2013 /media/Shared_Data/freesurfer/bin 2) After sourcing FreeSurfer, what happens when you type: tkmedit -f $SUBJECTS_DIR/sample-001.mgz shalim-ubunut:/media/Shared_Data/freesurfer tkmedit -f $SUBJECTS_DIR/sample-001.mgz /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit -f $SUBJECTS_DIR/sample-001.mgz [sudo] password for francesca: sudo: tkmedit: command not found 3) Does freeview open (just type 'freeview' after sourcing FreeSurfer)? shalim-ubunut:/media/Shared_Data/freesurfer freeview /media/Shared_Data/freesurfer/bin/freeview: Permission ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coomand not found
Sure, thanks! tcsh shalim-ubunut:/media/Shared_Data/freesurfer setenv FREESURFER_HOME /media/Shared_Data/freesurfer shalim-ubunut:/media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni shalim-ubunut:/media/Shared_Data/freesurfer pwd /media/Shared_Data/freesurfer shalim-ubunut:/media/Shared_Data/freesurfer tkmedit bert orig.mgz /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied. shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit bert orig.mgz sudo: tkmedit: command not found shalim-ubunut:/media/Shared_Data/freesurfer/bin ls -la tkmedit -rwxrwxrwx 1 francesca francesca 102 May 14 2013 tkmedit 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Ok, could you send the entire terminal output? Thanks. -Louis On Mon, 12 May 2014, Francesca Strappini wrote: Thanks Louis! Yes, I did run tkmedit from the same terminal window I have sourced freesurfer... Francesca 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automatically when opening a new terminal or setting up an alias to make the process quicker. -Louis On Sat, 10 May 2014, Francesca Strappini wrote: Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coomand not found
Thanks Louis! Yes, I did run tkmedit from the same terminal window I have sourced freesurfer... Francesca 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu: Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automatically when opening a new terminal or setting up an alias to make the process quicker. -Louis On Sat, 10 May 2014, Francesca Strappini wrote: Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coomand not found
Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] register data to the surface
Hi! I successfully run the preprocessing on some polarangle data (preproc-sess -sf seesid -surface self lhrh -fwhm 5). Now I would like to do the subtraction between some runs and then to visualize this subtraction on the surface (so without to analyze the data with Fourier analysis). Does anybody know how to do that? Thanks! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] register data to the surface
Sorry, I try to be more specific. I would like to be able to take the volume-to-surface transformation calculated on one set of functional data, and apply that transformation to another set of functional data (the subtraction) of the same subject. This will allow me to display arbitrary functional values on a surface. Thanks! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] register data to the surface
Thanks a lot! I tried the registration with bbregister but unfortunately when I checked the result the functional volume was very distant from the target. Could I tried something else to improve the registration? I typed: bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl --bold Thanks again! Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] full flat patch issue
Hi, I'm trying to create a full flat map. The process of flattening seems has finished without any errors, but I got this error message when I tried to show up the full flat patch: lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list Thanks a lot Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] anatomical ROI
Hi all, I would ask you about anatomical ROIs. I'm going to begin the analysis of some retinotopic data, my question is: when I draw the closed contours, does automatically my ROI contain the entire inner surface or just the outline? Thank you kindly in advance. Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] retinotopy: MGH vs UCSD
Hi all, I would ask you about freesurfer and retinotopy. I'm going to begin the analysis of some retinotopic data. I would ask if you know if the retinotopic analysis made by MGH freesurfer is qualitatively comparable to, or it's good as, that made by USCD freesurfer (old freesurfer). Thank you kindly in advance. Francesca ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] retinotopy: MGH vs UCSD
old freesurfer, or csurf, is this: http://kamares.ucsd.edu/~sereno/csurf/tarballs/ made by Marty Sereno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
