[Freesurfer] R: Re: R: import FS-FAST results in FSL

[stdp82]

Yes I would like to open with fslview (FSL) the sig.nii.gz of each 
subject which is computed by seed-based analysis by FS-FAST.
I have mask the sig.nii.gz by fslmaths -div
I have run:
mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg 
subj/rest/001/register.dof6.dat --hemi rh --o prova.nii.gz

but when I open the prova.nii.gz with fslview the windows is empty 
with a line.

Thanks


Stefano

>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 29-set-2015 22.09
>A: 
>Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL
>
>Do you mean surface-based analysis? You'd have to put them back into 
the 
>volume using mri_surf2vol, write them out as nifti and then run 
fslview 
>on them
>
>On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
>>
>> Hi list,
>>
>> I would like to import FS-FAST results (conjunction maps) in 
FSL,
>> opening them by fslview.
>> Could you provide me any suggestion?
>>
>> Thank you very much
>> Best regards,
>>
>>
>> Stefano
>>
>>
>>
>>
>> ___
>> 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

[Freesurfer] 3dClustSim and Gaussian filter width

[Emma Thompson]

Dear Freesurfers,
I am trying to use 3dclustsim in AFNI to determine the minimum number of
voxel in a cluster to reach significance, my understanding is that in the
command line the -fwhm s flag refers to the gaussian filter width and NOT
the Gaussian Kernel, can anyone point me to how I might be able to obtain
this for each hemisphere in freesurfer? I am using my own average brain
that I created, but it would help to know how to do this for the fsaverage
as well.

Many thanks for your help!


http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html
___
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] R: Re: R: import FS-FAST results in FSL

[Bruce Fischl]

Hi Stefano

mri_vol2surf samples the volume onto the surface and saves it as a 1D 
list of values, one per surface vertex. You can't view that in fslview 
AFAIK - you need to load a surface in freeview/tksurfer and visualize it 
as an overlay on the surface.

cheers
Bruce
On Tue, 27 Oct 2015, std...@virgilio.it wrote:

> Yes I would like to open with fslview (FSL) the sig.nii.gz of each
> subject which is computed by seed-based analysis by FS-FAST.
> I have mask the sig.nii.gz by fslmaths -div
> I have run:
> mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg
> subj/rest/001/register.dof6.dat --hemi rh --o prova.nii.gz
>
> but when I open the prova.nii.gz with fslview the windows is empty
> with a line.
>
> Thanks
>
>
> Stefano
>
>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 29-set-2015 22.09
>> A: 
>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL
>>
>> Do you mean surface-based analysis? You'd have to put them back into
> the
>> volume using mri_surf2vol, write them out as nifti and then run
> fslview
>> on them
>>
>> On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
>>>
>>> Hi list,
>>>
>>> I would like to import FS-FAST results (conjunction maps) in
> FSL,
>>> opening them by fslview.
>>> Could you provide me any suggestion?
>>>
>>> Thank you very much
>>> Best regards,
>>>
>>>
>>> Stefano
>>>
>>>
>>>
>>>
>>> ___
>>> 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
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] remove label from aseg

[Douglas Greve]

The indices should be different. Eg, 17 is left hippo, 53 is right
hippo. If you click on them in freeview and different labels appear,
then FS knows they are different

On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
> Hi.
>
> Just one another related question: now that I was able to combine left and
> right hippocampal subfields with the aparc-aseg correctly, I noticed that
> the left and right hippocampal subfields have the same color labels and
> codes. What would be the best way to make sure that FreeSurfer understand
> that the left and right subfields (e.g. Left and right CA1) are different
> areas? 
>
> Thanks!
> Heidi
>
> On 10/21/15, 11:01 PM, "Jacobs H (NP)" 
> wrote:
>
>> Thanks! Works wonderful!
>> Heidi
>>
>> On 10/21/15, 10:50 PM, "Douglas N Greve" 
>> wrote:
>>
>>> If you want to remove them, you can use mri_binarize with the --replace
>>> option, replacing them with whatever you want.
>>>
>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
 Hi,

 I am trying to generate a segmentation file containing the aseg+aparc
 but replacing the hippocampus with the hippocampal subfields.
 With mergeseg I was able to merge the segmentations, but unfortunately
 parts of the ³old² hippocampus (labeled as 17 and 53) are still in
 there (as the area covered by the subfields is not 100% equal to the
 hippocampus of the aseg).
 How can I remove the remains of the old hippocampal labels?

 Many thanks!
 Best
 Heidi


 ___
 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
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Funcroi-Table-Sess Error

[Douglas Greve]

I think the problem is probably that you created the label from a volume 
whereas funcroi expects the label to come from a surface. Instead of 
using mri_cor2label and  -label for funcroi-config, try using something like


funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant -analysis 
analysis_induc_block.lh-roi roiconfig_ACC_lh

On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:

Hi there,

I ran the following analysis commands:

 1. mri_cor2label --c
/autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id
11106 --l
/autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
 2. funcroi-config -labellabl_ACC_lh.label -analysis
analysis_induc_block.lh-roi roiconfig_ACC_lh
 3. funcroi-table-sess -analysis analysis_induc_block.lh -contrast
contrast_neg_V_neut -roi roiconfig_ACC_lh-sf
sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat


After running the 'funcroi-table-sess’ command I got the following error:

ERROR: There is a vertex in the label that cannot be matched to
the surface. This usually occurs when the label and surface are
from different subjects or hemispheres of the surface has been
changed since the label was created.


It seems that the problem might be that the command is using my 
participant (in this case, nmasa_001) as the source subject  BUT it’s 
using fsaverage as the target subject. I want the target subject to be 
my participant as well (not fsaverage).


Is there a way that I can specify the target subjects? Or is there a 
more efficient way do what I’m trying to do (ie: 1. generate labels 
for each participant based on their aparc+aseg file and 2. calculate 
the mean contrast signal from each ROI for each participant).


Thanks,
Keji


--- Morenikeji Adebayo Clinical Research Coordinator Department of 
Psychiatric Neuroscience
Massachusetts General Hospital (p) 
617.643.6347k...@nmr.mgh.harvard.edu 


___
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] comparison of 4 groups: mri_glmfit or Qdec?

[Douglas Greve]

yes, use mri_glmfit
doug

On 10/26/15 3:34 AM, Sandy Schramm wrote:
> Dear Experts,
>
> we want to compare data (thickness) of 4 groups (3 morbid groups and 1
> controll group). Both, Qdec and mri_glmfit, will do the same analyses.
> But we are not sure, if the usage of Qdec is statistically correct in
> our case. Because in Qdec we can only compare 2 of the 4 groups. But
> Qdec is much more comfortable to handle.
> Or do you advise the mri_glmfit for our data analyses?
>
> Thanks for some advice!
> Sandy Schramm
> ___
> 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] remove label from aseg

[Jacobs H (NP)]

Hi Doug,

Yes, for the aseg they are. But not for the hippocampal subfields: left
and right have the same color coding.
I am creating one segmentation, including left and right hippocampal
subfields and aparc, for partial volume correction.
Any idea how I can make the labels for the hippocampal subfields different
(freesurfer version 6)?

Thanks
Heidi

On 10/27/15, 4:32 PM, "Douglas Greve"  wrote:

>The indices should be different. Eg, 17 is left hippo, 53 is right
>hippo. If you click on them in freeview and different labels appear,
>then FS knows they are different
>
>On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>> Hi.
>>
>> Just one another related question: now that I was able to combine left
>>and
>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>>that
>> the left and right hippocampal subfields have the same color labels and
>> codes. What would be the best way to make sure that FreeSurfer
>>understand
>> that the left and right subfields (e.g. Left and right CA1) are
>>different
>> areas? 
>>
>> Thanks!
>> Heidi
>>
>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>
>> wrote:
>>
>>> Thanks! Works wonderful!
>>> Heidi
>>>
>>> On 10/21/15, 10:50 PM, "Douglas N Greve" 
>>> wrote:
>>>
 If you want to remove them, you can use mri_binarize with the
--replace
 option, replacing them with whatever you want.

 On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
> Hi,
>
> I am trying to generate a segmentation file containing the aseg+aparc
> but replacing the hippocampus with the hippocampal subfields.
> With mergeseg I was able to merge the segmentations, but
>unfortunately
> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
> there (as the area covered by the subfields is not 100% equal to the
> hippocampus of the aseg).
> How can I remove the remains of the old hippocampal labels?
>
> Many thanks!
> Best
> Heidi
>
>
> ___
> 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
>>
>>
>
>___
>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] Centrum Semiovale Labels in Freesurfer

[Douglas Greve]

We changed the name to "unsegmented white matter" because we don't know 
whether they really represent centrum semiovale. We don't have an ROI  
that has been verified to be CS.

doug

On 10/25/15 7:10 PM, Syeda Maryam wrote:

Hello Freesurfer experts,

I needed to extract the centrum semiovale from freesurfer labels to 
use for further analysis. The freesurfer website states that the 
Centrum semiovale is labeled with 5001 (left) and 5002 (right). I 
found these labels in the wmparc.mgz volume, however they are labeled 
as left/right unsegmented white matter. Do these still correspond to 
the centrum semiovale?


Thanks in advance for your help!

Maryam


___
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] hippocampal subfield viewing

[Danielle Miller]

Hello,

I used recon-all -hippo subfields on an earlier version of free surfer
(recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website
on how to view the subfields in freeview with versions earlier than 5.2. I
noticed when I load all the subfields into free view and use the color LUT
file, the subfields have pixelated colors at each voxel. Is there a way to
view earlier versions of this similar to what is presented on the website
(i.e., where subfields are represented by solid colors)? I assume this may
be an issue with intensity values in the image?

Thanks,
Danielle

-- 
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118


VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave  D11-103
Boston, MA 02130
OFFICE:(857) 364-2130
___
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] QDEC output after Monte Carlo simulation

[Douglas Greve]

It may cover both, but the peak can only be in one, and it is the peak 
that is reported.



On 10/25/15 9:55 AM, Annemarie Brandhofe wrote:

Dear freesurfer experts,

I have analyzed inter-group differences in cortical thickness using 
freesurfer 5.3.0 and QDEC. I have found one significiant cluster in 
the medialorbitofrontal region that is corrected for multiple 
comparisons using Monte Carlo simulation (p<0,05) and listed in the 
qdec output file "mc-z.abs.th13.abs.sig.cluster.summary". However, the 
cluster shown in the display window of Qdec is located both in the 
lateralorbitofrontal and the medialorbitofrontal region.
Why is the lateralorbitofrontal region not mentioned in the file 
"mc-z.abs.th13.abs.sig.cluster.summary"?


I have attached the contents of the output file and a screenshot of 
the display window of QDEC after the Monte Carlo simulation.


Thank you in advance for your help.

Anne




___
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] remove label from aseg

[Douglas Greve]

The color is not important. The question is whether they have a
different index. Can you confirm that lh and rh have the same index?

On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
> Hi Doug,
>
> Yes, for the aseg they are. But not for the hippocampal subfields: left
> and right have the same color coding.
> I am creating one segmentation, including left and right hippocampal
> subfields and aparc, for partial volume correction.
> Any idea how I can make the labels for the hippocampal subfields different
> (freesurfer version 6)?
>
> Thanks
> Heidi
>
> On 10/27/15, 4:32 PM, "Douglas Greve"  wrote:
>
>> The indices should be different. Eg, 17 is left hippo, 53 is right
>> hippo. If you click on them in freeview and different labels appear,
>> then FS knows they are different
>>
>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>> Hi.
>>>
>>> Just one another related question: now that I was able to combine left
>>> and
>>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>>> that
>>> the left and right hippocampal subfields have the same color labels and
>>> codes. What would be the best way to make sure that FreeSurfer
>>> understand
>>> that the left and right subfields (e.g. Left and right CA1) are
>>> different
>>> areas? 
>>>
>>> Thanks!
>>> Heidi
>>>
>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>> 
>>> wrote:
>>>
 Thanks! Works wonderful!
 Heidi

 On 10/21/15, 10:50 PM, "Douglas N Greve" 
 wrote:

> If you want to remove them, you can use mri_binarize with the
> --replace
> option, replacing them with whatever you want.
>
> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>> Hi,
>>
>> I am trying to generate a segmentation file containing the aseg+aparc
>> but replacing the hippocampus with the hippocampal subfields.
>> With mergeseg I was able to merge the segmentations, but
>> unfortunately
>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>> there (as the area covered by the subfields is not 100% equal to the
>> hippocampus of the aseg).
>> How can I remove the remains of the old hippocampal labels?
>>
>> Many thanks!
>> Best
>> Heidi
>>
>>
>> ___
>> 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
>>>
>>>
>> ___
>> 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] hippocampal subfield viewing

[Eugenio Iglesias]

Hi Danielle, 

from the mri directory of a subject, run 

freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz 
-p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix 
posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt 

and be a bit patient; it takes a little while to combine all the posteriors 
into the segmentation. 

Cheers, 

Eugenio 




Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Danielle Miller"  
To: "Freesurfer support list"  
Sent: Tuesday, October 27, 2015 4:40:57 PM 
Subject: [Freesurfer] hippocampal subfield viewing 


Hello, 

I used recon-all -hippo subfields on an earlier version of free surfer (recon v 
5.0, hippo v5.0 or 5.1). There is no documentation on your website on how to 
view the subfields in freeview with versions earlier than 5.2. I noticed when I 
load all the subfields into free view and use the color LUT file, the subfields 
have pixelated colors at each voxel. Is there a way to view earlier versions of 
this similar to what is presented on the website (i.e., where subfields are 
represented by solid colors)? I assume this may be an issue with intensity 
values in the image? 

Thanks, 
Danielle 

-- 
Ph.D. Program in Behavioral Neuroscience 
Boston University School of Medicine L-815 
72 E. Concord St 
Boston, MA 02118 


VA Boston Healthcare System Jamaica Plain 
Memory Disorders Research Center 
150 South Huntington Ave D11-103 
Boston, MA 02130 
OFFICE:(857) 364-2130 


___ 
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.

Re: [Freesurfer] remove label from aseg

[Jacobs H (NP)]

I just checked again in freeview and indeed they have the same index (e.g.
CA1 has value 206 for left and also for right).

On 10/27/15, 5:01 PM, "Douglas Greve"  wrote:

>The color is not important. The question is whether they have a
>different index. Can you confirm that lh and rh have the same index?
>
>On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>> Hi Doug,
>>
>> Yes, for the aseg they are. But not for the hippocampal subfields: left
>> and right have the same color coding.
>> I am creating one segmentation, including left and right hippocampal
>> subfields and aparc, for partial volume correction.
>> Any idea how I can make the labels for the hippocampal subfields
>>different
>> (freesurfer version 6)?
>>
>> Thanks
>> Heidi
>>
>> On 10/27/15, 4:32 PM, "Douglas Greve"  wrote:
>>
>>> The indices should be different. Eg, 17 is left hippo, 53 is right
>>> hippo. If you click on them in freeview and different labels appear,
>>> then FS knows they are different
>>>
>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
 Hi.

 Just one another related question: now that I was able to combine left
 and
 right hippocampal subfields with the aparc-aseg correctly, I noticed
 that
 the left and right hippocampal subfields have the same color labels
and
 codes. What would be the best way to make sure that FreeSurfer
 understand
 that the left and right subfields (e.g. Left and right CA1) are
 different
 areas? 

 Thanks!
 Heidi

 On 10/21/15, 11:01 PM, "Jacobs H (NP)"
 
 wrote:

> Thanks! Works wonderful!
> Heidi
>
> On 10/21/15, 10:50 PM, "Douglas N Greve" 
> wrote:
>
>> If you want to remove them, you can use mri_binarize with the
>> --replace
>> option, replacing them with whatever you want.
>>
>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>> Hi,
>>>
>>> I am trying to generate a segmentation file containing the
>>>aseg+aparc
>>> but replacing the hippocampus with the hippocampal subfields.
>>> With mergeseg I was able to merge the segmentations, but
>>> unfortunately
>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>>> there (as the area covered by the subfields is not 100% equal to
>>>the
>>> hippocampus of the aseg).
>>> How can I remove the remains of the old hippocampal labels?
>>>
>>> Many thanks!
>>> Best
>>> Heidi
>>>
>>>
>>> ___
>>> 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


>>> ___
>>> 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

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[pablo najt]

Thank you for your input. I noticed that if I follow literally all the steps in 
the wiki, my data which is ordered by variable 'family' (instead of subjects, 
in my case is number of members belonging to e.g. family_1) is shuffled. This 
happens after I run the command sortData below. Especially I noticed that ni 
and X do not match sID.It would be really helpful to know what is this command 
doing. I am wondering whether my data differs in number of columns or else and 
because of this I end with a shuffled data. Any suggestion or tips to figure 
what could be happening?ThanksPablo
[M, Y, ni] = sortData(M,1,Y,sID)
To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Wed, 14 Oct 2015 10:54:41 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}


  

  
  
Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)
see

https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels 



hope that helps, Martin





On 10/14/2015 10:43 AM, pablo najt
  wrote:



  

Dear FS experts.
  I have query about a relating to a previous email
(below). I am aiming to run a
  LME analysis on cross-sectional data from different
  families and have variable 'family' (number of families)
  as my NI vector. 
  My design has three groups and therefore I am not able to
use qdec. I am running the matlab commands below and finding
some difficulty would really appreciate if you could help
out.
  Thanks
  Pablo
  


  Start analysis as follows:
  

  
  1-Read your label eg.:

  lhcortex = 
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');

  2-Read the data file eg.:

  [lhY, lhmri] = fs_read_Y('lh.thickness.mgh'); 

  
 %-I input the concatenated .mgh image from 
preproc and 
mris_surf2surf---%


  
  3-Fit a vertex-wise lme model with random effects.:

  lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); 

  
Here I am getting the following problems:
% If I use number of families as my ni get the 
following%
  


  

  
lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);
  

  
  

  
Error using lme_mass_fit (line 108)
  

  
  

  
The total number of measurements, indicated by sum(ni), mustbe 
the same as the number of rows of the design
  

  
  

  
matrix X
  

  
  

  


  

  
  

  
Error in lme_mass_fit_vw (line 73)
  

  
  

  
[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);


  

  


  
 My matrix is organised in "family", "group", Sex" and "age" 
columns".


  
4-Perform vertex-wise inference eg.:
CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats, CM);
5-Save results eg.: 
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');  

Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset

Hi Pablo

I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni'  vector is equal to the
number of different families in your data.  





Now you can go
further and additionally order the rows of your design matrix within
each family by age. This will allow you to test the effect of age
within family. 





When choosing the
random effects for your statistical 

[Freesurfer] T1-coregistered fmri - output to .nii

[Parker, Richard]

Hi Freesurfers,


I am interested in running a functional connectivity analysis outside of the 
Freesurfer environment, using freesurfer-derived ROIs


I've run recon-all, and I have run preproc-sess to carry out initial fmri 
preprocessing steps (motion correction, warping to the anatomical, etc)


Next, I need to produce a .nii version of the T1-coregistered (and slice time 
corrected) fMRI timecourse, which I don't believe is created by preproc-sess.



I've tried applying the register.dof6.dat to the motion corrected functional 
timeseries with mri_vol2vol, but the output is upsampled to the space of the T1 
(and also is rotated 90 degrees, a phenomenon already discussed in several 
previous posts, I believe). I'm trying to produce a co-registered (but not 
upsampled) timeseries.


Final point: another forum post details a process whereby T1-ROIs can be warped 
to the space of the native, non-coregistered fMRI data. This isn't appropriate 
for my analysis unfortunately, as I am running a multi-modal analysis, whereby 
everything needs to be in alignment with the T1.


Any help would be greatly appreciated!


Best wishes,


Richard




Richard Parker
Postgraduate Research Student

Maurice Wohl Clinical Neuroscience Institute
King's College London

Telephone: 07943515208
Email: richard.r.par...@kcl.ac.uk
___
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] Funcroi-Table-Sess Error

[Douglas Greve]

On 10/27/15 1:09 PM, Morenikeji Adebayo wrote:

Hi Doug,

Thanks for the help!  So, you’re saying that:

 1. By specifying  a volume file (ie: aparc.a2009s+aseg.mgz) when
using mri_cor2label, I’ve created volume labels


Correct


 1. The commands ‘funcroi-config' and 'funcroi-table-sess' accept only
labels created on the surface.

It takes either. But the analysis you use is a surface-based analysis, 
so you need a surface-based label.

doug


Is this correct?
Thanks,
Keji

On Oct 27, 2015, at 11:38 AM, Douglas Greve 
> wrote:


I think the problem is probably that you created the label from a 
volume whereas funcroi expects the label to come from a surface. 
Instead of using mri_cor2label and  -label for funcroi-config, try 
using something like


funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant -analysis 
analysis_induc_block.lh-roi roiconfig_ACC_lh

On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:

Hi there,

I ran the following analysis commands:

 1. mri_cor2label --c
/autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz
--id 11106 --l
/autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
 2. funcroi-config -labellabl_ACC_lh.label -analysis
analysis_induc_block.lh-roi roiconfig_ACC_lh
 3. funcroi-table-sess -analysis analysis_induc_block.lh -contrast
contrast_neg_V_neut -roi roiconfig_ACC_lh-sf
sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat


After running the 'funcroi-table-sess’ command I got the following 
error:


ERROR: There is a vertex in the label that cannot be matched to
the surface. This usually occurs when the label and surface are
from different subjects or hemispheres of the surface has been
changed since the label was created.


It seems that the problem might be that the command is using my 
participant (in this case, nmasa_001) as the source subject  BUT 
it’s using fsaverage as the target subject. I want the target 
subject to be my participant as well (not fsaverage).


Is there a way that I can specify the target subjects? Or is there a 
more efficient way do what I’m trying to do (ie: 1. generate labels 
for each participant based on their aparc+aseg file and 2. calculate 
the mean contrast signal from each ROI for each participant).


Thanks,
Keji


--- Morenikeji Adebayo Clinical Research Coordinator Department of 
Psychiatric Neuroscience
Massachusetts General Hospital (p) 
617.643.6347k...@nmr.mgh.harvard.edu 


___
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
--- Morenikeji Adebayo Clinical Research Coordinator Department of 
Psychiatric Neuroscience
Massachusetts General Hospital (p) 
617.643.6347k...@nmr.mgh.harvard.edu 


___
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] Minc-tools - cannot find required library hdf5 - Ubuntu 12.04

[Bruno LAD]

Hi everybody. Could anyone help me please?

I've downloaded minc-tools source code to compile and install on Ubuntu
12.04, but I've got an error when try to run the *configure* file.


The log is below:

root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# ./configure
--prefix=/root/freesurfer-inst --enable-static
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc and cc understand -c and -o together... yes
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for sys/stat.h... (cached) yes
checking sys/wait.h usability... yes
checking sys/wait.h presence... yes
checking for sys/wait.h... yes
checking for unistd.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking for int32_t... yes
checking for int16_t... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether gfortran accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static 

Re: [Freesurfer] Funcroi-Table-Sess Error

[Morenikeji Adebayo]

Hi Doug,

Thanks for the help!  So, you’re saying that:

By specifying  a volume file (ie: aparc.a2009s+aseg.mgz) when using 
mri_cor2label, I’ve created volume labels
 The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels 
created on the surface.

Is this correct?

Thanks,
Keji


> On Oct 27, 2015, at 11:38 AM, Douglas Greve  wrote:
> 
> I think the problem is probably that you created the label from a volume 
> whereas funcroi expects the label to come from a surface. Instead of using 
> mri_cor2label and  -label for funcroi-config, try using something like
> 
> funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant  -analysis 
> analysis_induc_block.lh -roi roiconfig_ACC_lh
> 
> 
> 
> On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:
>> Hi there,
>> 
>> I ran the following analysis commands:
>> 
>>  mri_cor2label --c 
>> /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 
>> 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
>> funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh 
>> -roi roiconfig_ACC_lh
>> funcroi-table-sess -analysis analysis_induc_block.lh -contrast 
>> contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o 
>> sumtable_ACC_lh.dat
>> 
>> After running the 'funcroi-table-sess’ command I got the following error:
>> 
>> ERROR: There is a vertex in the label that cannot be matched to the surface. 
>> This usually occurs when the label and surface are from different subjects 
>> or hemispheres of the surface has been changed since the label was created.
>> 
>> It seems that the problem might be that the command is using my participant 
>> (in this case, nmasa_001) as the source subject  BUT it’s using fsaverage as 
>> the target subject. I want the target subject to be my participant as well 
>> (not fsaverage).
>> 
>> Is there a way that I can specify the target subjects? Or is there a more 
>> efficient way do what I’m trying to do (ie: 1. generate labels for each 
>> participant based on their aparc+aseg file and 2. calculate the mean 
>> contrast signal from each ROI for each participant).
>> 
>> 
>> Thanks,
>> Keji
>> 
>> 
>> 
>> --- Morenikeji Adebayo Clinical Research Coordinator Department of 
>> Psychiatric Neuroscience
>> Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu 
>> 
>> ___
>> 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

---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.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 - minc lib not found - Ubuntu 12.04

[Bruno LAD]

Hi everybody. Could anyone help me please?

I've downloaded FreeSurfer source code to compile and install on Ubuntu
12.04, but I've got an error when try to run the *configure* file.


The log is below:

root@ubuntu:~/freesurfer-source/freesurfer# ./configure
--prefix=/root/freesurfer-inst --enable-static
configure: Setting System...
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking AMD Open64 compiler directories... Open64 directory is not supplied
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gawk... (cached) gawk
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... file_magic ELF
[0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking for file... /usr/bin/file
checking if gcc static flag  works... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... no
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking dynamic linker characteristics... GNU/Linux ld.so
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... 

[Freesurfer] mri_parse_sdcmdir splitting a single series into two?

[Oliver Hinds]

Hi,

I'm running into an issue where the slices from one DICOM series are being
parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate
series.

A few example lines from a scan.out:

  6  AR_t.s40.c0  ok   64  64  41   1 
  7  AR_t.s40.c0  ok   64  64  23   1 

The scan AR_t.s40.c0 was run as a single series on the scanner, with 64
slices. Inspection of the dicom header shows that the series UID is the
same for the DICOM files in each, except there is an extra string '.0.0.0'
at the end of series UID in the DICOMS that are parsed into the second
series.

Has anyone else experienced this behavior? If so, is there a workaround?

Thanks,
Oliver


___
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] Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study

[Don Hagler]

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study

 

University of California, San Diego

 

Several funded postdoctoral positions are available in image analysis method 
development, including automated cortical- and subcortical segmentation, 
advanced diffusion tractography, and fMRI mapping and time series analysis. We 
are looking to build a team to help build the next generation of analysis 
pipelines and visualization tools for a newly funded study to follow 10,000 
children with longitudinal structural and functional imaging across 19 sites 
across the US. The study will use a cross-platform Harmonized Human Connectome 
Protocol, optimized for quantitative accuracy and consistency of imaging 
biomarkers across scanners and time. To learn more about the ABCD study, please 
see 
http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain-development
 
.

 

Requirements: Applicants should have research experience in any of the above 
fields, with a Ph.D. or equivalent degree. They should be comfortable working 
in a distributed team environment, and should have a track record of quality 
scientific publications. Candidates are expected to be experienced in 
programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, 
FSL, and the Human Connectome analysis pipelines is strongly preferred.

 

To formally apply, submit a current CV, a personal statement describing your 
research experience and interests, and contact information for 2-3 references 
to a...@ucsd.edu . Or feel free to email Dr. Donald 
Hagler (dhag...@ucsd.edu ) or Anders M. Dale 
(amd...@ucsd.edu ) for more information.

 

The University of California, San Diego is an Equal Opportunity/Affirmative 
Action Employer advancing inclusive excellence. All qualified applicants will 
receive consideration for employment without regard to race, color, religion, 
sex, sexual orientation, gender identity, national origin, disability, age, 
protected veteran status, or other protected categories covered by the UC 
nondiscrimination policy.___
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 pve correction tool

[Mohamed Ali Bahri]

Dear Bruce,

Am I missed the answer of Dr. Greve about the following questions?

Is it possible to tell what are the implemented methods for the PET pve 
correction? and how we can
obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?


Many thanks,

Mohamed



On 26/10/15 14:52, Bruce Fischl wrote:
> oh, then I'll leave it for Doug
> Bruce
> On Mon, 26 Oct 2015, Mohamed Ali Bahri
> wrote:
>
>> Hi Bruce,
>>
>> Yes, for PET analysis.
>>
>> Best,
>>
>> Mohamed
>>
>> On 26/10/15 14:45, Bruce Fischl wrote:
>>> Hi Mohamed
>>>
>>> do you mean for PET analysis or for the recent paper that Rebecca Shafee
>>> wrote on e.g. tissue intensity properties?
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
>>>
 Is it possible to tell what are the implemented methods? and how we can
 obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?

 Best,

 Mohamed

 On 26/10/15 13:27, Bruce Fischl wrote:
> no, sorry, we haven't had time to document it
> On Mon, 26 Oct 2015,
> m.ba...@ulg.ac.be wrote:
>
>> Dear FreeSurfer Experts,
>>
>> Are there any documentation comes out for the pve correction tool 
>> implemented in the FreeSurfer V6?
>>
>> Many thanks in advance,
>>
>> Best,
>>
>> Mohamed
>> ___
>> 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

-- 
Dr. Mohamed Ali Bahri,
1er Logisticien de Recherche,
Cyclotron Research Centre,
University of Liège, Belgium
m.ba...@ulg.ac.be

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[Martin Reuter]

Hi Pablo,

the sortData function sorts the rows so that entries from the same 
subject (in your case same family) are blocked and that within each 
block the time variable (2nd parameter specifies which column that is in 
your M matrix, in your case the first =1) is increasing.
It is important, when creating your design matrix X, that ordering 
agrees with Y. That is guaranteed if you generate X from M (which is 
ordered like Y after the sort command).


Best, Martin

On 10/27/2015 01:32 PM, pablo najt wrote:

Thank you for your input.
I noticed that if I follow literally all the steps in the wiki, my 
data which is ordered by variable 'family' (instead of subjects, in my 
case is number of members belonging to e.g. family_1) is shuffled. 
This happens after I run the command sortData below. Especially I 
noticed that ni and X do not match sID.
It would be really helpful to know what is this command doing. I am 
wondering whether my data differs in number of columns or else and 
because of this I end with a shuffled data. Any suggestion or tips to 
figure what could be happening?

Thanks
Pablo

[M, Y, ni] = sortData(M,1,Y,sID)


To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Wed, 14 Oct 2015 10:54:41 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within 
subject dataset {Disarmed}


Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)
see
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

hope that helps, Martin


On 10/14/2015 10:43 AM, pablo najt wrote:

Dear FS experts.
I have query about a relating to a previous email (below). I am
aiming to run a LME analysis on cross-sectional data from
different families and have variable 'family' (number of families)
as my NI vector.
My design has three groups and therefore I am not able to use
qdec. I am running the matlab commands below and finding some
difficulty would really appreciate if you could help out.
Thanks
Pablo

Start analysis as follows:

1-Read your label eg.:
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');

%-I input the concatenated .mgh image from
preproc and

mris_surf2surf---%

3-Fit a vertex-wise lme model with random effects.:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Here I am getting the following problems:

% If I use number of families as my ni get
the

following%

lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);

Error using lme_mass_fit (line 108)

The total number of measurements, indicated by
sum(ni), mustbe the same as the number of rows of the
design

matrix X

Error in lme_mass_fit_vw (line 73)

[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

My matrix is organised in "family", "group", Sex" and "age"
columns".

4-Perform vertex-wise inference eg.: CM.C = [your contrast
matrix]; F_lhstats = lme_mass_F(lhstats, CM); 5-Save results eg.:
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');


Date: Thu, 10 Sep 2015 13:44:36 + From: jbernal0...@yahoo.es
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer]
A mixed effect model approach in within subject dataset
Hi Pablo
I think you can use LME to analyze your data by ordering the rows
of your design matrix appropriately. You can consider all subjects
belonging to the same family as if they were a single subject in a
longitudinal analysis. You can put in your design matrix all
subjects belonging to family1 first, then all subjects belonging
to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw
is a vector with the number of subjects in each family as its
entries (ordered according to your design matrix). So the length
of the 'ni' vector is equal to the number of different families in
your data.
Now you can go further and additionally order the rows of your
design matrix within each family by age. This will allow you to
test the effect of age within family.
When choosing the random effects for your statistical model
remember that a random effect can only be the intercept term or
any covariate that varies within family. For example 

Re: [Freesurfer] FreeSurfer pve correction tool

[Douglas N Greve]

Hi Mohamed, sorry, I have not fully documented the procedure yet. I've 
put some notes below
doug


1. To start, run

gtmseg --s subject

This will take a couple of hours and produces some files needed for GTM 
PVC (which is used for GTM, MG, RBV).

2. You'd then register the PET to the anatomical with bbregister (with 
--t2 weighting). Make sure to save the output as an LTA (--lta). I 
usually use the mean TAC as the input. You can do this in parallel with #1.

3. You'd then run mri_gtmpvc, something like

mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg 
gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output 
--km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale

PSF is the point-spread FWHM of the scanner; reg.lta is the registration 
from #2.  --km-hb specifies the highbinding region for MRTM2. --km-ref 
specifies the reference region.  --mgx specifies to output a 
muller-gartner map (not necessary for GTM ROI analysis).

4. For the GTM (ROI) MRTM1 KM analysis, you would then run

  mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o 
mrtm1 --no-est-fwhm --nii.gz

where time.dat is a text file withe acquisition time of each time point 
in the tac.

5. For the MRTM2 analysis

set k2p = `cat mrtm1/k2prime.dat`
mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o 
mrtm1 --no-est-fwhm --nii.gz

If you want to run a voxel-wise analysis, then you can use the mgx
volume as input (--y). Probably you'll want to sample this to the
surface using mri_vol2surf and the registration file aux/anat2pet.lta,
then smooth on the surface




On 10/27/2015 04:47 PM, Mohamed Ali Bahri wrote:
> Dear Bruce,
>
> Am I missed the answer of Dr. Greve about the following questions?
>
> Is it possible to tell what are the implemented methods for the PET pve 
> correction? and how we can
> obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?
>
>
> Many thanks,
>
> Mohamed
>
>
>
> On 26/10/15 14:52, Bruce Fischl wrote:
>> oh, then I'll leave it for Doug
>> Bruce
>> On Mon, 26 Oct 2015, Mohamed Ali Bahri
>> wrote:
>>
>>> Hi Bruce,
>>>
>>> Yes, for PET analysis.
>>>
>>> Best,
>>>
>>> Mohamed
>>>
>>> On 26/10/15 14:45, Bruce Fischl wrote:
 Hi Mohamed

 do you mean for PET analysis or for the recent paper that Rebecca Shafee
 wrote on e.g. tissue intensity properties?

 cheers
 Bruce



 On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:

> Is it possible to tell what are the implemented methods? and how we can
> obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
>
> Best,
>
> Mohamed
>
> On 26/10/15 13:27, Bruce Fischl wrote:
>> no, sorry, we haven't had time to document it
>> On Mon, 26 Oct 2015,
>> m.ba...@ulg.ac.be wrote:
>>
>>> Dear FreeSurfer Experts,
>>>
>>> Are there any documentation comes out for the pve correction tool 
>>> implemented in the FreeSurfer V6?
>>>
>>> Many thanks in advance,
>>>
>>> Best,
>>>
>>> Mohamed
>>> ___
>>> 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

-- 
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