[Freesurfer] Cohen's D Multiple Comparisons
Dear FreeSurfer experts, For my group-level analyses, I created Cohen's D effect size maps. Now I looking the different methods to correct for multiple comparisons (FDR and MC-simulations), it seems to me they are based on p-values, not on effect sizes. I tried applying FDR-correction in tksurfer on the effect size maps. This indeed results in a higher threshold for clusters to appear, but I am not sure whether this is a valid tool to use in statistical maps other than .sig ? As a p-value reflects the chances of finding this effect by chance and the MC-correction is about reducing the chance of false positives, and Cohen's D not reflecting such chances, is correction for multiple comparisons even sound when reporting effect sizes? If so, what would be the best approach to determine an MC-corrected threshold for effect sizes? Thanks again for your help, you have been very helpful so far! Best wishes, Lizanne ___ 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_anatomical_stats aparc pial and aparcstats2table
Hi Louis, It didn't work either. This is what shows up in the terminal after running mris_anatomical_stats: mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.aparc.annot. reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial... reading input pial surface /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ./aparc.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1272793 2092 2.485 0.342 0.141 0.042 24 2.4 bankssts 1184957 2200 2.419 0.757 0.226 0.187 24811.5 caudalanteriorcingulate 3222 2408 5307 2.324 0.512 0.136 0.040 58 4.8 caudalmiddlefrontal 2468 1735 2917 1.798 0.388 0.150 0.064 54 5.2 cuneus 504582 1801 3.807 0.663 0.256 0.084 24 2.0 entorhinal 4892 3757 9658 2.696 0.715 0.183 0.073 16715.0 fusiform 8153 6383 13887 2.315 0.543 0.160 0.049 17916.6 inferiorparietal 4885 3695 10298 2.929 0.668 0.171 0.069 18714.8 inferiortemporal 1470 1045 2169 2.137 0.673 0.200 0.129 154 8.8 isthmuscingulate 6612 4848 10068 2.208 0.530 0.161 0.058 21715.6 lateraloccipital 3665 2871 6467 2.380 0.684 0.186 0.067 12311.1 lateralorbitofrontal 4593 3224 5598 1.811 0.528 0.170 0.072 16513.4 lingual 2623 2020 4262 2.290 0.776 0.191 0.072 179 8.1 medialorbitofrontal 4570 3991 10068 2.785 0.605 0.169 0.052 15410.0 middletemporal 1041802 1923 2.621 0.705 0.161 0.058 20 2.4 parahippocampal 2067 1415 2808 2.156 0.580 0.115 0.024 20 2.1 paracentral 1534 1130 2779 2.551 0.445 0.149 0.042 29 2.5 parsopercularis 1366 1265 2718 2.458 0.607 0.184 0.049 23 2.9 parsorbitalis 2166 1826 3699 2.258 0.484 0.166 0.048 34 4.8 parstriangularis 2637 1647 2528 1.563 0.436 0.137 0.043 47 4.7 pericalcarine 6180 4524 7746 1.879 0.596 0.122 0.030 62 7.3 postcentral 1694 1270 2783 2.265 0.721 0.188 0.088 64 7.6 posteriorcingulate 7118 5162 11283 2.336 0.590 0.115 0.027 67 8.4 precentral 5554 4071 8657 2.206 0.527 0.149 0.051 10812.8 precuneus 975856 2003 2.660 0.591 0.167 0.063 27 2.8 rostralanteriorcingulate 8524 6942 13736 2.121 0.581 0.163 0.047 16816.2 rostralmiddlefrontal 9820 7927 17866 2.426 0.605 0.150 0.043 14416.4 superiorfrontal 8910 6920 12666 1.952 0.561 0.134 0.033 10211.5 superiorparietal 5164 4064 9880 2.602 0.579 0.141 0.041 129 8.5 superiortemporal 4538 3307 6832 2.129 0.591 0.140 0.035 63 6.4 supramarginal 395426864 2.488 0.541 0.199 0.0576 0.9 frontalpole 612699 2018 3.610 0.559 0.213 0.073 17 2.2 temporalpole 479330680 2.330 0.353 0.110 0.0243 0.5 transversetemporal 3442 1950 6183 2.886 0.890 0.376 1.131 154 291.0 insula [user@localhost label]$ aparcstats2table --hemi rh --subjects FERNANDORODRIGUES --parc aparcpial --meas area -t rh_FERNANDORODRIGUES.aparc.surface.pial.txt Number of subjects : 1 Building the table.. ERROR: cannot find /home/user/visao/Freesurfer/FERNANDORODRIGUES/stats/rh.aparcpial.stats Use --skip flag if you want to continue in such cases Maybe is the mris_anatomical_stats that has something wrong? I've been using the command for Brodmann Areas and just tried to adapt it to aparc. For BA I've also had to run label2label and had to create a new BA.annot but that was because I had to get the thresholded BA values, I think this doesn't apply to aparc. From aparc I only want to get
[Freesurfer] space conversion in the mri_surf2vol
Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123___ 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] space conversion in the mri_surf2vol
Hi Rujing we need your entire command line to know cheers Bruce On Thu, 27 Mar 2014, charujing123 wrote: Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123 ___ 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] space conversion in the mri_surf2vol
Hi Bruce It's mri_surf2vol --surfval ./lh.gender_age.thickness.10.mgh --hemi rh --fillribbon --subject fsaverage --identity fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o test.nii Thanks All the best. Rujing Zha 2014-03-27 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-03-27 20:32 主题：Re: [Freesurfer] space conversion in the mri_surf2vol 收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu 抄送： Hi Rujing we need your entire command line to know cheers Bruce On Thu, 27 Mar 2014, charujing123 wrote: Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123 ___ 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 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] recon error
Hi, I got this error while running recon-all : 'imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: mpr2mni305 execution aborted Any idea what could be the cause? Thanks,Xiaomin Yue ___ 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_preproc patch download
Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation takes me to ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc where a script appears. I thought that it would take me to a download page of some type of file that I would use to substitute the mrs_preproc I have now. How should I proceed? Copy and the paste the script text in my current mris_preproc (deleting what is now written) and then save and run qcache. Or, since I already have FS 5.3 installed in a different location, can I simply copy and paste the 5.3 mris_preproc file replacing the 5.0 one? I predict that both approaches are equivalent but I want to be completely sure that I'll be doing it in the right way. Thanks, Andreia ___ 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] adding time points to longitudinal base template {Disarmed} {Disarmed} {Disarmed}
Thanks Martin, I tried that on version 5.1 and it worked.
Regards
Koushik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Tuesday, March 25, 2014 9:55 AM
To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
{Disarmed} {Disarmed}
Hi Koushik,
there seems to be a bug. There's a safety check (that usually makes sense) but
when adding a tp, of course it is not yet contained in the base.
Fix it by:
For Version 5.3 change the line 6148 in recon-all from
if ( ! $found_tpNid ) then
to
if ( ! $found_tpNid ! $DoAddTp ) then
for 5.1 change line 5407 from
if ($status) then
to
if ( $status ! $DoAddTp ) then
Good luck, Martin
On 03/19/2014 12:56 PM, Govindarajan, Koushik Athreya wrote:
Hi Martin,
I use version 5.1. I did try this with version 5.3 also but I end up with
the same error:
recon-all -long 23061_ip cr096_base -addtp -all
ERROR: 23061_ip is not in /home/koushikg/data/longitudinal/cr096_base/base-tps
Thanks
Koushik
From:
freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Wednesday, March 19, 2014 11:21 AM
To: Govindarajan, Koushik Athreya;
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
{Disarmed}
Hi Koushik,
What version are you using? Not sure when we added this, maybe in 5.2. So you
would need 5.3 for it.
If you use 5.3 already, can you send me the exact command and output.
Thanks, Martin
On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote:
Hi Martin,
I tried this method of -addtp to add a new time point but recon-all
failed with the message saying my new timepoint was not in the 'base-tps' file
of the base template. Should I be doing something else before I run this step?
Thanks
Koushik
From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 9:31 AM
To: Govindarajan, Koushik Athreya;
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik,
there is a way to add time points without recreating the base:
recon-all -long tpNsubjid longbasesubjid -addtp -all
This is what the recon-all help says about that:
If a new timepoint needs to be added to a longitudinal run where a base subject
has already been created (from prior timepoints), then the -addtp command
can be added to the -long command in order to 'fix-up' the longitudinal
stream to accept the new timepoint. Note that the base subject is *not*
recomputed using the new timepoint. This potentially introduces a bias, and it
is recommended to NOT add a time point this way! Instead recreate the base
from all time points and run all longitudinals again.
So it's up to you. But given you already have 5 time points in your base and
add only 1, you may be fine. The base should be pretty stable with 5 and if the
6th is not too different, it should not matter much. I don't think anyone has
ever done a thorough analysis about adding time points.
Best, Martin
On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote:
Dear FS experts,
I have a serial study in which I have run cross-sectional and
longitudinal analysis on 5 time points. Now, I want to add a 6th time point to
my dataset. Do I have to rerun my base template creation step from scratch or
is there a way to just add further time points to an existing template?
Thanks
Koushik
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[Freesurfer] mri_glmfit-sim error
Hello list, I'm working with FS 5.0.3. When I used 'mri_glmfit-sim --glmdir /home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs --cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a mri_glmfit.log in folder /.../g2.lh, and copied this file to folder /.../g2.lh/C1/.But i still got an error 'fwhm: Undefined variable.' Can anybody help me settle this problem? Thank you! - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.5.0-23-generic x86_64 ___ 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] Fwd: Problem about the fMRI Analysis?
Dear Sir, I get the correlation result between two condition of the functional data by using AFNI( I do not know how to do correlation by using freesurfer). And then I use the bbregister to aline the correlation result (produce by Afni) to the anatomical result produced by using freesurfer(recon-all). Next I using mri_vol2surf to aline the each one's functional result to the fsaverage offer by freesurfer. My question is : I have two group of subjects. I want to get the correlation different between them? What should I do next by using freesurfer? I want to know how to calculate the correlation between two group by using freesurfer based on the surface-based analysis? Thanks very much! Linda ___ 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_preproc patch download
download the file and copy it into $FREESURFER_HOME/bin and make it executable (make a backup first) On 03/27/2014 09:37 AM, _andre...@sapo.pt wrote: Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation takes me to ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc where a script appears. I thought that it would take me to a download page of some type of file that I would use to substitute the mrs_preproc I have now. How should I proceed? Copy and the paste the script text in my current mris_preproc (deleting what is now written) and then save and run qcache. Or, since I already have FS 5.3 installed in a different location, can I simply copy and paste the 5.3 mris_preproc file replacing the 5.0 one? I predict that both approaches are equivalent but I want to be completely sure that I'll be doing it in the right way. Thanks, Andreia ___ 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.
Re: [Freesurfer] MNI CONVERSION PROBLEM
The first one should be correct. How are you visualizing it? What is the
command line?
On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
I have used both for the output of mni152reg:
mri_vol2vol --mov
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --targ
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--inv --o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz
and
mri_vol2vol --targ
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --mov
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz
I also have tried these two commands with the output matrix of
bbregister s001_register.dat
- Mensaje original -
De: Douglas Greve gr...@nmr.mgh.harvard.edu
Fecha: Jueves, 27 de Marzo de 2014, 4:11 am
Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
A: freesurfer@nmr.mgh.harvard.edu
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric
labels of my subjects extracted with mris_extract_label in FS v.5.1
but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them give me
an example to check at the registrations using tktegister2, when I
use it everything seems to be OK, but when I do apply with
mri_vol2vol any of the matrices to the volumetric masks, they appear
to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced,
Gabriel
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font size=3--br /PhD. student Gabriel
González-Escamillabr /Laboratory of Functional Neurosciencebr
/Department of Physiology, Anatomy, and Cell Biologybr /University
Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr
/- Spain -br /br /Email: ggon...@upo.esbr
/http://www.upo.es/neuroaging/es//font
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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Re: [Freesurfer] Cohen's D Multiple Comparisons
I don't think it makes sense to correct using cohen's d. I've never heard of it at least doug On 03/27/2014 06:31 AM, L. Schweren wrote: Dear FreeSurfer experts, For my group-level analyses, I created Cohen’s D effect size maps. Now I looking the different methods to correct for multiple comparisons (FDR and MC-simulations), it seems to me they are based on p-values, not on effect sizes. I tried applying FDR-correction in tksurfer on the effect size maps. This indeed results in a higher threshold for clusters to appear, but I am not sure whether this is a valid tool to use in statistical maps other than .sig ? As a p-value reflects the “chances” of finding this effect by chance and the MC-correction is about reducing the “chance of false positives”, and Cohen’s D not reflecting such chances, is correction for multiple comparisons even sound when reporting effect sizes? If so, what would be the best approach to determine an MC-corrected threshold for effect sizes? Thanks again for your help, you have been very helpful so far! Best wishes, Lizanne ___ 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.
Re: [Freesurfer] Problem with license for running mris_make_face_parcellation
Is it world-readable? Run chmod a+r $FREESURFER_HOME/license.txt On 03/27/2014 12:41 PM, Mahshid Najafi wrote: Hi Douglas, I tried copying it to $FREESURFER_HOME/license.txt but did not work.. On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi mhs...@gmail.com mailto:mhs...@gmail.com wrote: Hi, I have an openSUSE 12.2 (x86_64) and my freesurfer version is freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/Mahshid/fsl When I run freeview, it works correctly, but when I try to run tkmedit and mris_make_face_parcellation it gives following error: -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- I updated the .license recently and tried some suggestion previously uploaded on mailing list, but none worked. Would you please let me know how to solve it? my .license is: mhs...@gmail.com mailto:mhs...@gmail.com 17259 *CJUIGOoAoZws Thanks, Mahshid ___ 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.
[Freesurfer] (no subject)
Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse clicks (load atlas -- click on one label -- save selected label), but I'm just wondering if there is any existing freesurfer command line that can save labels from the terminal (assuming that the index and names of the labels are known)? Thanks so much for any help! Best, Qing ___ 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] MNI CONVERSION PROBLEM
I have tried several thing like opening on MriCroN and tkregister as:
tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg
/root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat
- Mensaje original -
De: Douglas N Greve gr...@nmr.mgh.harvard.edu
Fecha: Jueves, 27 de Marzo de 2014, 5:54 pm
Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
A: freesurfer@nmr.mgh.harvard.edu
The first one should be correct. How are you visualizing it?
What is the
command line?
On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
I have used both for the output of mni152reg:
mri_vol2vol --mov
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
targ
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--inv --o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz
and
mri_vol2vol --targ
/root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
mov
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz
I also have tried these two commands with the output matrix of
bbregister s001_register.dat
- Mensaje original -
De: Douglas Greve gr...@nmr.mgh.harvard.edu
Fecha: Jueves, 27 de Marzo de 2014, 4:11 am
Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
A: freesurfer@nmr.mgh.harvard.edu
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some
volumetric
labels of my subjects extracted with mris_extract_label in FS
v.5.1
but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them
give me
an example to check at the registrations using tktegister2,
when I
use it everything seems to be OK, but when I do apply with
mri_vol2vol any of the matrices to the volumetric masks, they
appear
to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced,
Gabriel
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font size=3--br /PhD.
student Gabriel
González-Escamillabr /Laboratory of Functional
Neurosciencebr
/Department of Physiology, Anatomy, and Cell Biologybr
/University
Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 -
Sevillebr
/- Spain -br /br /Email: ggon...@upo.esbr
/http://www.upo.es/neuroaging/es//font
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--
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/
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font size=3--br /PhD. student Gabriel
González-Escamillabr /Laboratory of Functional Neurosciencebr /Department
of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr
/Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email:
ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font
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Re: [Freesurfer] mris_preproc patch download
Hi Doug, I had to Save file as... So, that was the download... Backup made and mris_preproc replaced by the new one. Thank you! Andreia Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: download the file and copy it into $FREESURFER_HOME/bin and make it executable (make a backup first) On 03/27/2014 09:37 AM, _andre...@sapo.pt wrote: Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation takes me to ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc where a script appears. I thought that it would take me to a download page of some type of file that I would use to substitute the mrs_preproc I have now. How should I proceed? Copy and the paste the script text in my current mris_preproc (deleting what is now written) and then save and run qcache. Or, since I already have FS 5.3 installed in a different location, can I simply copy and paste the 5.3 mris_preproc file replacing the 5.0 one? I predict that both approaches are equivalent but I want to be completely sure that I'll be doing it in the right way. Thanks, Andreia ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with license for running mris_make_face_parcellation
Hi Douglas, I tried copying it to $FREESURFER_HOME/license.txt but did not work.. On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi mhs...@gmail.com wrote: Hi, I have an openSUSE 12.2 (x86_64) and my freesurfer version is freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/Mahshid/fsl When I run freeview, it works correctly, but when I try to run tkmedit and mris_make_face_parcellation it gives following error: -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- I updated the .license recently and tried some suggestion previously uploaded on mailing list, but none worked. Would you please let me know how to solve it? my .license is: mhs...@gmail.com 17259 *CJUIGOoAoZws Thanks, Mahshid ___ 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] saving labels from the terminal?
Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse clicks (load atlas -- click on one label -- save selected label), but I'm just wondering if there is any existing freesurfer command line that can save labels from the terminal (assuming that the index and names of the labels are known)? Thanks so much for any help and sorry that I forgot to add subject in my previous email! Best, Qing ___ 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] space conversion in the mri_surf2vol
The mgh file is a surface overlay, not a 3d volume. The nii will be in MNI305 space On 03/27/2014 08:36 AM, charujing123 wrote: Hi Bruce It's mri_surf2vol --surfval ./lh.gender_age.thickness.10.mgh --hemi rh --fillribbon --subject fsaverage --identity fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o test.nii Thanks All the best. Rujing Zha 2014-03-27 charujing123 *发件人：*Bruce Fischl fis...@nmr.mgh.harvard.edu *发送时间：*2014-03-27 20:32 *主题：*Re: [Freesurfer] space conversion in the mri_surf2vol *收件人：*Freesurfer support listfreesurfer@nmr.mgh.harvard.edu *抄送：* Hi Rujing we need your entire command line to know cheers Bruce On Thu, 27 Mar 2014, charujing123 wrote: Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123 ___ 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 -- 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
Re: [Freesurfer] Problem with license for running mris_make_face_parcellation
Yes it is, and I run it, but still receive the error. On Thu, Mar 27, 2014 at 12:41 PM, Mahshid Najafi mhs...@gmail.com wrote: Hi Douglas, I tried copying it to $FREESURFER_HOME/license.txt but did not work.. On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi mhs...@gmail.com wrote: Hi, I have an openSUSE 12.2 (x86_64) and my freesurfer version is freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/Mahshid/fsl When I run freeview, it works correctly, but when I try to run tkmedit and mris_make_face_parcellation it gives following error: -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- I updated the .license recently and tried some suggestion previously uploaded on mailing list, but none worked. Would you please let me know how to solve it? my .license is: mhs...@gmail.com 17259 *CJUIGOoAoZws Thanks, Mahshid ___ 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] Problem with license for running mris_make_face_parcellation
Please provide the output when you type: ls -l $FREESURFER_HOME/license.txt on the command line. Thanks. -Zeke On 03/27/2014 02:20 PM, Mahshid Najafi wrote: Yes it is, and I run it, but still receive the error. On Thu, Mar 27, 2014 at 12:41 PM, Mahshid Najafi mhs...@gmail.com mailto:mhs...@gmail.com wrote: Hi Douglas, I tried copying it to $FREESURFER_HOME/license.txt but did not work.. On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi mhs...@gmail.com mailto:mhs...@gmail.com wrote: Hi, I have an openSUSE 12.2 (x86_64) and my freesurfer version is freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/Mahshid/fsl When I run freeview, it works correctly, but when I try to run tkmedit and mris_make_face_parcellation it gives following error: -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- I updated the .license recently and tried some suggestion previously uploaded on mailing list, but none worked. Would you please let me know how to solve it? my .license is: mhs...@gmail.com mailto:mhs...@gmail.com 17259 *CJUIGOoAoZws Thanks, Mahshid ___ 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.
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Hi Pedro Sorry, right now the only multiple comparisons corrections implemented in lme are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure (lme_mass_FDR2): Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear step-up procedures that control the false discovery rate. Biometrika, 93, 491-507. In my experience, this procedure is as powerful to detect effects in neuroimage data as alternative corrections with strong control of the family-wise error rate (FWE). However it would be great if we could use an implementation of any multiple comparisons correction with strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures only provide weak control). The residual errors at each location required to compute an estimate of the image FWHM can be obtained from the lme output. But an actual FWHM estimate is not currently saved. Best -Jorge El Martes 25 de marzo de 2014 8:15, Pedro Rosa pedrogomesr...@gmail.com escribió: Dear Doug, Thank you very much! I will try what you suggested, although I am not sure if Jorge's stream outputs the FMHM, or if I would need to run the statistics from the beggining using in the terminal, and not in MatLab. Do you think Jorge could comment on this issue? Regards, Pedro Rosa. On Mar 24, 2014, at 12:44 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: In theory, it should be possible. I have not used Jorge's stream, so I don't know that much about it. Does it save an estimate of the FWHM? If so, then you can run mri_surfcluster passing it the p-value (ie, -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is what mri_glmfit-sim does, so you might check that script for mri_surfcluster command line options doug On 3/22/14 11:03 PM, Pedro Rosa wrote: Dear list, I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a structural MRI dataset and I would like to use Monte Carlo as the method for correction for multiple comparisons. However, the longitudinal LME tutorial includes only FDR correction (lme_mass_FDR2). Is it possible to use Monte Carlo correction for longitudinal data? Can I input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and then run Monte Carlo? If not, do you have any other suggestions of how I use Monte Carlo in longitudinal analyses? Thanks in advance, ___ 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 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] mc-bbr
Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.html) to do this (named mc-bbr). But I am not sure if it is valid any more and not sure how does it works. As far as I see, there is no flag for mc-bbr or something similar to that in preproc-sess. I appreciate if you guide me through it. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Problem with license for running mris_make_face_parcellation
The output is: -rw-rw-rw- 1 Mahshid users 36 Mar 27 12:37 license.txt ___ 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] Problem about the fMRI Analysis?
Dear Douglas, I do not understand what's your meaning? Yes I think the afni results has already alined to T1.mgz, so it is already in talairach space. I do not know what to do next? As I have two groups subjects. I do not know what to analysis the correlation different between two groups by using surface-based analysis of freesurfer. Linda Message: 5 Date: Wed, 26 Mar 2014 14:05:46 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem about the fMRI Analysis? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 533316fa.50...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Are the AFNI results already in talairach space? If so, then there is no point in going to surface space. doug On 03/26/2014 01:22 PM, Linda Xu wrote: I get the correlation result between two condition of the functional data by using AFNI( I do not know how to do correlation by using freesurfer) And then I use the bbregister to aline the correlation result (produce by Afni) to the anatomical result produced by using freesurfer. Next I using mri_vol2surf to aline the each one's functional result to the fsaverage offer by freesurfer. My question is :1 Should I need to do mri_vol2vol next for each subject? 2 I have two group of subjects. I want to know if there is some correlation different between them? What should I do next? Thanks very much! Linda ___ 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] Problem about the fMRI Analysis?
Surface-based analysis is an alternative to talairach-based analysis. It does not make sense to do both. Is the AFNI talairach space affine (ie, 12 dof)? If so, then it is possible to undo the resampling to talairach space. You will need to know which space the afni results are in (ie, MNI152 or MNI305 or something else? 1mm or 2mm?) doug On 3/27/14 5:06 PM, Linda Xu wrote: Dear Douglas, I do not understand what's your meaning? Yes I think the afni results has already alined to T1.mgz, so it is already in talairach space. I do not know what to do next? As I have two groups subjects. I do not know what to analysis the correlation different between two groups by using surface-based analysis of freesurfer. Linda Message: 5 Date: Wed, 26 Mar 2014 14:05:46 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem about the fMRI Analysis? To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 533316fa.50...@nmr.mgh.harvard.edu mailto:533316fa.50...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Are the AFNI results already in talairach space? If so, then there is no point in going to surface space. doug On 03/26/2014 01:22 PM, Linda Xu wrote: I get the correlation result between two condition of the functional data by using AFNI( I do not know how to do correlation by using freesurfer) And then I use the bbregister to aline the correlation result (produce by Afni) to the anatomical result produced by using freesurfer. Next I using mri_vol2surf to aline the each one's functional result to the fsaverage offer by freesurfer. My question is :1 Should I need to do mri_vol2vol next for each subject? 2 I have two group of subjects. I want to know if there is some correlation different between them? What should I do next? Thanks very much! Linda ___ 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] mc-bbr
This is not something that was ever ready for use. doug On 3/27/14 3:22 PM, SHAHIN NASR wrote: Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.html) to do this (named mc-bbr). But I am not sure if it is valid any more and not sure how does it works. As far as I see, there is no flag for mc-bbr or something similar to that in preproc-sess. I appreciate if you guide me through it. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Extracting ROI information using created label
Hi, We are having some trouble extracting ROI (thickness) information using a label we created. After conducting a group analysis, we drew an ROI label based on the results. We used tksurfer to draw the label (we couldn't do this in freeview, which would freeze for some reason). However, at this point we're kind of stuck. The tutorial slides give the way to extract ROI information using existing labels, and then how to create a label, but not how to use the custom label to extract the relevant information. Any advice would be appreciated! Thanks, Clint -- I remain... Clinton L. Johns, Ph.D. Research Scientist, Haskins Laboratories 300 George Street New Haven CT 06511 speech: 203-865-6163 x240 fax: 203-865-8963 net: jo...@haskins.yale.edu ___ 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] freesurfer install
Hi freesurfer， I ?installed the package of freesurfer according to the intruction of freesurfer website. But when I checked whether it was installed successfully, I inputed?the commands following: 1)?tksurfer bert rh pial? Couldn't create output file .xdebug_tksurfersubject is bert hemiis rh surface is pial 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/bin surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz 2) tkmedit bert orig.mgz?Couldn't create output file .xdebug_tkmedit === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : 3) ?qdec?qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory yxk-ThinkStation-D30:/usr/local/freesurfer/bin ? Thus, I want to know the reason why these problems occurred, and the solution to these problems. Thank you very much Meng___ 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] error
Dear experts, when I run the qdec, and the wrong information appear in following: qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory I hope some experts to help me ,thank you very much! -- Bo Xiang State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China The Mental Health Center and the Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China Phone: +8615281056345 QQ: 529111494 Skype: xiang.bo3 向波 四川大学华西医院生物治疗国家重点实验室，华西医院精神医学研究室 成都市武侯区人民南路三段中四川大学华西校区，610041 E-mail: xiangbo_2...@126.com / xiangboyulan2...@gmail.com 电话：15281056345 QQ：529111494 Skype：xiang.bo3 ___ 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.
