Re: [Freesurfer] feat to qdec

[Christophe de Bezenac]

Hi Doug

Thanks for responding.  in my path. I actually now managed to 
run it but it fails at the   command (Command not found). 

/Users/chdebezenac
flirt.fsl -ref 
/Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
 -in 
/Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii
 -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
-90 90 -verbose 0 -omat 
/Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat
 -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init 
/Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat
flirt.fsl: Command not found.
ERROR: flirt

Do you or anyone else know why that might be the case?

Thanks,
Christophe

 



On 5 Nov 2013, at 23:18, Douglas N Greve wrote:

> Is reg-feat2anat in your path? It should be in 
> $FREESURFER_HOME/bin/reg-feat2anat
> doug
> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
>> Hi everyone,
>> 
>> I am very new to freesurfer/qdec. What I would like to do is examine the 
>> results of a feat analysis in qdec and then perform further between-subject 
>> analyses with behavioural data 
>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). 
>> I've run against problems at the first stage (registration) 
>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical).
>>  I imagine something is not set up right?
>> 
>> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh
>> setenv FREESURFER_HOME freesurfer
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv FREESURFER_HOME 
>> freesurfer
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source 
>> freesurfer/SetUpFreeSurfer.csh
>>  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   freesurfer
>> FSFAST_HOME   freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  freesurfer/subjects
>> MNI_DIR   freesurfer/mni
>> FSL_DIR   /usr/local/fsl
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR 
>> freesurferX/subjects
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% cd 
>> scan1Cor.feat
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>> chdebezenac% ln -s $SUBJECTS_DIR/fsaverage
>> ln: ./fsaverage: File exists
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>> chdebezenac% ln -s $SUBJECTS_DIR/S1
>> ln: ./S1: File exists
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>> chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
>> reg-feat2anat: Command not found.
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>> chdebezenac% cd
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% ls
>> S1   S4  fbert   lh.EC_average   scan1Cor.feat
>> S2   S5  fbert2.feat qdec
>> S3   bertfsaverage   rh.EC_average
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
>> reg-feat2anat --feat scan1Cor.feat --subject S1
>> reg-feat2anat: Command not found.
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac%
>> 
>> Any help would be greatly appreciated,
>> 
>> Christophe
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
>> 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 
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http

Re: [Freesurfer] feat to qdec

[Douglas N Greve]

That should also be in $FREESURFER_HOME/bin. If not, just copy or 
symlink your flirt program to it.
doug

ps. Please remember to post to the FS list and not to me personally. thanks!



On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
> Thanks for responding Doug,
>
>  is in my path. I've actually now managed to run 
>  till the  command which produces the error 
> (Command not found).
>
> /Users/chdebezenac
> flirt.fsl -ref 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
>  -in 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii
>  -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
> -90 90 -verbose 0 -omat 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat
>  -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat
> flirt.fsl: Command not found.
> ERROR: flirt
>
> Do you know why this might be?
>
> Thanks again,
> Christophe
>
>
>
> On 5 Nov 2013, at 23:18, Douglas N Greve wrote:
>
>> Is reg-feat2anat in your path? It should be in
>> $FREESURFER_HOME/bin/reg-feat2anat
>> doug
>> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
>>> Hi everyone,
>>>
>>> I am very new to freesurfer/qdec. What I would like to do is examine the 
>>> results of a feat analysis in qdec and then perform further between-subject 
>>> analyses with behavioural data 
>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). 
>>> I've run against problems at the first stage (registration) 
>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical).
>>>  I imagine something is not set up right?
>>>
>>> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh
>>> setenv FREESURFER_HOME freesurfer
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv FREESURFER_HOME 
>>> freesurfer
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source 
>>> freesurfer/SetUpFreeSurfer.csh
>>>  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> FREESURFER_HOME   freesurfer
>>> FSFAST_HOME   freesurfer/fsfast
>>> FSF_OUTPUT_FORMAT nii.gz
>>> SUBJECTS_DIR  freesurfer/subjects
>>> MNI_DIR   freesurfer/mni
>>> FSL_DIR   /usr/local/fsl
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR 
>>> freesurferX/subjects
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% cd 
>>> scan1Cor.feat
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>>> chdebezenac% ln -s $SUBJECTS_DIR/fsaverage
>>> ln: ./fsaverage: File exists
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>>> chdebezenac% ln -s $SUBJECTS_DIR/S1
>>> ln: ./S1: File exists
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>>> chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
>>> reg-feat2anat: Command not found.
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
>>> chdebezenac% cd
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% ls
>>> S1  S4  fbert   lh.EC_average   scan1Cor.feat
>>> S2  S5  fbert2.feat qdec
>>> S3  bertfsaverage   rh.EC_average
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
>>> reg-feat2anat --feat scan1Cor.feat --subject S1
>>> reg-feat2anat: Command not found.
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac%
>>>
>>> Any help would be greatly appreciated,
>>>
>>> Christophe
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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 contac

Re: [Freesurfer] feat to qdec

[Douglas N Greve]

oops, sorry I just noticed that you did respond to the list!

On 11/06/2013 10:16 AM, Douglas N Greve wrote:
> That should also be in $FREESURFER_HOME/bin. If not, just copy or
> symlink your flirt program to it.
> doug
>
> ps. Please remember to post to the FS list and not to me personally. thanks!
>
>
>
> On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
>> Thanks for responding Doug,
>>
>>  is in my path. I've actually now managed to run 
>>  till the  command which produces the error 
>> (Command not found).
>>
>> /Users/chdebezenac
>> flirt.fsl -ref 
>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
>>  -in 
>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii
>>  -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
>> -90 90 -verbose 0 -omat 
>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat
>>  -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init 
>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat
>> flirt.fsl: Command not found.
>> ERROR: flirt
>>
>> Do you know why this might be?
>>
>> Thanks again,
>> Christophe
>>
>>
>>
>> On 5 Nov 2013, at 23:18, Douglas N Greve wrote:
>>
>>> Is reg-feat2anat in your path? It should be in
>>> $FREESURFER_HOME/bin/reg-feat2anat
>>> doug
>>> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
 Hi everyone,

 I am very new to freesurfer/qdec. What I would like to do is examine the 
 results of a feat analysis in qdec and then perform further 
 between-subject analyses with behavioural data 
 (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). 
 I've run against problems at the first stage (registration) 
 (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical).
  I imagine something is not set up right?

 Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh
 setenv FREESURFER_HOME freesurfer
 [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv FREESURFER_HOME 
 freesurfer
 [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source 
 freesurfer/SetUpFreeSurfer.csh
  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   freesurfer
 FSFAST_HOME   freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii.gz
 SUBJECTS_DIR  freesurfer/subjects
 MNI_DIR   freesurfer/mni
 FSL_DIR   /usr/local/fsl
 [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR 
 freesurferX/subjects
 [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
 cd scan1Cor.feat
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
 chdebezenac% ln -s $SUBJECTS_DIR/fsaverage
 ln: ./fsaverage: File exists
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
 chdebezenac% ln -s $SUBJECTS_DIR/S1
 ln: ./S1: File exists
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
 chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
 reg-feat2anat: Command not found.
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
 chdebezenac% cd
 [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% ls
 S1 S4  fbert   lh.EC_average   scan1Cor.feat
 S2 S5  fbert2.feat qdec
 S3 bertfsaverage   rh.EC_average
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
 reg-feat2anat --feat scan1Cor.feat --subject S1
 reg-feat2anat: Command not found.
 [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac%

 Any help would be greatly appreciated,

 Christophe









 ___
 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

Re: [Freesurfer] How do you create labels from binary masks?

[Douglas N Greve]

So is the problem that the annotation does not look good or is the 
problem that you are getting a lot of warnings about unmapped vertices. 
Please send the command lines that generate the warnings (and the 
terminal output)
doug


On 11/06/2013 10:05 AM, Marcos Martins da Silva wrote:
> Hi, Doug
> Thanks again for your help.
> I am really glad to say I managed to get the labels and annotation 
> file I wanted. See attached screenshot for result. There is one final 
> problem I will explain ahead. The parameter that made this possible 
> was *--ref*. So the final mri_vol2surf that made the trick was:
>
> mri_vol2surf --src binLeftHippoTail.mgz --out LeftHippoTail_surf.mgh 
> --out_type mgh --hemi lh --regheader suj1 --surf surfHippo 
> --projdist-max -2 0 .1 *--ref* binLeftHippoTail.mgz
>
> This way, using my binary mask both as source and reference I got the 
> correct surface overlay to use as input in:
>
> mri_cor2label --i LeftHippoTail_surf.mgh --surf suj1 lh surfHippo --id 
> 1 --l lh.HippoTail.label
>
> The --projdist parameter you suggested resulted in a a better image so 
> I kept. Repeating this sequence for head and body I got what I wanted. 
> It seems the problem was related to differences in space among the 
> hipocampal subfields filesand orig.mgz (the default reference) perhaps 
> because the first files are 0.5 x 0.5 x 0.5 mm^3 and orig.mgz is 1 x 1 
> x 1 mm^3 or because the hippocampal subfields are generated from a 
> strict region around the original hippocampal segments you find in 
> aseg.mgz.
> Both Freeview and tksurfer can load the labels with no error message. 
> Both can load the annotation file too. But at terminal window they 
> show lots of vertices out of index (that is, present in lh.hippo.annot 
> and absent in lh.surfHippo). Labels seem ok with about 12000 vertices 
> if I sum the number of vertices in the 3 files because some vertices 
> are present in more than 1 label but annot includes a huge amount of 
> vertices mapped to unknown. It follows mris_info output.
>
> *mris_info --s suj1 lh surfHippo --a ../label/lh.Hippo.annot *
> *ERROR: ../label/lh.Hippo.annot has 122886 vertices, while 
> /home/marcos/freesurfer/subjects/suj1/surf/lh.surfHippo has 11627 
> vertices*
>
> It seems that mris_label2annot include a lot of unnecessary unknown 
> vertices not present in my surface nor in the labels during its 
> processing. It does not avoid using the annotation file but produces a 
> huge amount of warning lines at terminal window. I guess 
> mris)label2annot is using some other file as reference and seeing a I 
> did not see any parameter I could add to restrict this behavior. I 
> guess if I had something equivalent to --ref parameter as seem in 
> mri_vol2surf I could have a better result. Alternatively, if I could 
> process the annot file to trim the unmapped vertices I guess it would 
> work too.
> This is the mris_label2annot I am using:
>
> *mris_label2annot --s suj1 --h lh --ctab ../label/Hippo.ctab --a Hippo 
> --l ../label/lh.HippoHead.label --l ../label/lh.HippoBody.label --l 
> ../label/lh.HippoTail.label --maxstatwinner*
>
> I hope you can help me in this final issue so we can finnish this 
> thread. Thank you once more for your attention
> Cheers,
> Marcos.
> Em Seg, 2013-11-04 às 18:28 -0500, Douglas N Greve escreveu:
>> That vol2surf command might miss the values you want to sample. Try
>> adding --projdist-max -2 0 .1
>> This will sample from 2mm into the hippo out to the surface in .1mm
>> increments and then take the maximum value it finds
>> doug
>>
>> On 10/30/2013 03:08 PM, Marcos Martins da Silva wrote:
>> > Hi, Doug.
>> > Thanks again for all your attention.
>> > I am trying to show the head, body and tail segments on the
>> > hippocampal surface. Each with one color. I thought the best way to do
>> > it would be creating an annot file with 3 surface labels one for each
>> > segment. The approach, concatenation of hippo-subfields -> binarize ->
>> > tesselation -> smooth, I used gave me a realistic hippocampal surface.
>> > I could also segment that concatenated volume into head, body and tail
>> > but I do not know how to convert these segments into surface labels.
>> >
>> > Unfortunately mapping on the hippo surface did not work too, unless I
>> > did something wrong. Could you please check if the following commands
>> > are correct? Perhaps all I need is to add or remove one parameter.
>> >
>> > *mri_vol2surf --src binLeftHippoBody.mgz --out LeftHippoBody_surf.mgh
>> > --out_type mgh --hemi lh --regheader suj1 --surf surfHippo*
>> > *mri_cor2label --i LeftHippoBody_surf.mgh --surf suj1 lh surfHippo
>> > --id 1 --l lh.HippoBody.label*
>> >
>> > Cheers,
>> > Marcos.
>> >
>> >
>> > Em Qua, 2013-10-30 às 10:47 -0400, Douglas N Greve escreveu:
>> >> I've lost track of what you are trying to do. Can you just sample it on
>> >> to your hippo surface?
>> >> doug
>> >>
>> >>
>> >>
>> >> On 10/29/2013 08:05 PM, Marcos Martins da Silva wrote:
>> >> > I di

Re: [Freesurfer] glmfit for paired-diff on 2 groups

[Vivian R. Steiger]

Hi Doug

Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in the 
mailinglist


Commands:


mris_preproc  --target 1_average_30VPs  --fsgd responder.txt  --hemi lh 
 --meas thickness  --out respnon_lh_thickness.mgh —paired-diff-norm

mri_surf2surf --hemi lh --s 1_average_30VPs --fwhm 25 --sval 
respnon_lh_thickness.mgh --cortex --tval respnon_lh_thickness.sm25.mgh

mri_glmfit  --y respnon_lh_thickness.sm25.mgh --fsgd 
responder_paired.txt doss --C sad_groups.txt --surf 1_average_30VPs lh --cortex 
--glmdir  respnon_lh_thickness



FSGD 1: (responder.txt)

GroupDescriptorFile 1
Title Resonder_NonResponder
Class resp
Class nonresp
Input 1Pre_VP02.long.VP02_Base resp
Input 2Post_VP02.long.VP02_Base resp
Input 1Pre_VP03.long.VP03_Base nonresp
Input 2Post_VP03.long.VP03_Base nonresp
Input 1Pre_VP04.long.VP04_Base resp
Input 2Post_VP04.long.VP04_Base resp
Input 1Pre_VP05.long.VP05_Base nonresp
Input 2Post_VP05.long.VP05_Base nonresp
Input 1Pre_VP06.long.VP06_Base resp
Input 2Post_VP06.long.VP06_Base resp
Input 1Pre_VP07.long.VP07_Base resp
Input 2Post_VP07.long.VP07_Base resp
Input 1Pre_VP08.long.VP08_Base resp
Input 2Post_VP08.long.VP08_Base resp
Input 1Pre_VP09.long.VP09_Base resp
Input 2Post_VP09.long.VP09_Base resp
Input 1Pre_VP10.long.VP10_Base nonresp
Input 2Post_VP10.long.VP10_Base nonresp
.
.
.


FSGD 2: (responder_paired.txt)

GroupDescriptorFile 1
Class resp
Class nonresp
Input VP02pair resp
Input VP03pair nonresp
Input VP04pair resp
Input VP05pair nonresp
Input VP06pair resp
Input VP07pair resp
Input VP08pair resp
Input VP09pair resp
Input VP10pair nonresp
.
.
.


Best,
Vivian



_
On 11/04/2013 03:34 PM, Douglas N Greve wrote:
>Yes, that looks correct, though I could be more confident if you send 
>the command lines used and your fsgd file(s).
>doug


_
On 10/31/2013 07:32 AM, Vivian R. Steiger wrote:
> Dear FS-Experts,
>
> I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11)) 
> with longitudinal data.
> Participants from both groups had only 2 scan sessions in each case 10 weeks 
> apart.
>
> So far is used the glmfit-variant with --paired-diff option in the first 
> place. (based on 
http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
)
>
> The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is 
> used in glm-fit for comparison with the contrast (1 -1) for group diffs.
>
> This approach confirmed our hypothesized effects but I'm not sure whether I 
> used the right strategy.
>
> Could you might help me with this issue?
>
> Thank in advance
>
>
> Best,
>
> Vivian
>
>
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[Freesurfer] mri_label2vol not working

[Zhao Jingjing]

Hi Doug,

I have tried the command that you suggested below. Still not working.
System gave the same error message again "segment fault".

Any other ideas?

Best wishes,
Jingjing

*
try running this command
mri_label2vol --label lh.words10_10.label --temp rawavg.mgz --reg
rawreg.dat --fillthresh .5 --o lh.words10_10.nii

*
On 11/04/2013 07:55 AM, Zhao Jingjing wrote:
> Hi Doug,
>
> I asked a question a couple days ago for how to convert .label files
> into .nii files in freesurfer. At the end of this email, you can see
> the original email from me and your response.
>
> I tried to run the function mri_label2vol by myself. However, it seems
> not working quite well.
>
> In order to run mri_label2vol, it seems that I have to have a
> registration.dat file. I search online for how to generate it and get
> an answer from maillinglist posted by you several years ago. That is,
> I need to run the function of tkregister2. Then I tried to find out
> how to run tkregister2 and I found out an example suggested by you,
> although I don't know how it works because there is no information
> online for this function.
>
> Your example is like this:
>
> *tkregister2 --mov rawavg.mgz --targ aseg.mgz --regheader
> --regrawreg.dat --noedit*
>
>
> I ran it and it successfully generated a rawreg.dat file, but I don't
> know if it is a correct file that I should use. Below is the results
> that I got from the command window:
>
> *tkregister_tcl /opt/freesurfer/lib/tcl/
tkregister2.tcl
> target  volume aseg.mgz
> movable volume rawavg.mgz
> reg file   rawreg.dat
> LoadVol0
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $
> Diagnostic Level -1
> INFO: loading target aseg.mgz
> Ttarg: 
> -1.000   0.000   0.000   128.000;
>  0.000   0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> INFO: loading movable rawavg.mgz
> Tmov: 
> -0.900   0.000   0.000   100.799;
>  0.000   0.000   0.898  -115.000;
>  0.000  -0.898   0.000   115.000;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 1, float2int = 0
> Computing reg from header (and possibly input matrix)
>  Input registration matrix (computed) 
> -1.000  -0.012  -0.025  -0.000;
> -0.025   0.069   0.997   0.000;
>  0.010  -0.998   0.070  -0.000;
>  0.000   0.000   0.000   1.000;
> ---
>  Input registration matrix 
> -1.000  -0.012  -0.025  -0.000;
> -0.025   0.069   0.997   0.000;
>  0.010  -0.998   0.070  -0.000;
>  0.000   0.000   0.000   1.000;
> Determinant -1
> subject = subject-unknown
> RegMat ---
> -1.000  -0.012  -0.025  -0.000;
> -0.025   0.069   0.997   0.000;
>  0.010  -0.998   0.070  -0.000;
>  0.000   0.000   0.000   1.000;*
>
> Then I tried to run the function of mri_label2vol. I specifically
> referred to the example posted online in freesurfer website. It seems
> to me that this is a popular function that a lot of people have used.
> My command line is as below:
>
> *mri_label2vol --label lh.words10_10.label --temp T1.mgz --reg
> rawreg.dat --fillthresh .5 --o lh.words10_10.nii*
>
>
> However, my command line didn't run successfully to generate the nii
> file that I want. The error message is "segmentation flaut". Here I
> attached all the results from the command window after I run this
> function.
>
> *Number of labels: 1
> lh.words10_10.label
> Annot File:  (null)
> Template Volume: T1.mgz
> Outut Volume: lh.words10_10.nii
> Registration File: rawreg.dat
> Fill Threshold: 0.5
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> $Id: mri_label2vol.c,v 1.32 2009/10/22 23:35:53 greve Exp $
> Template RAS-to-Vox: 
> -1.000   0.000   0.000   128.000;
> -0.000  -0.000  -1.000   128.000;
> -0.000   1.000  -0.000   128.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1
> nHits Thresh: 0.5
> Loading registration from rawreg.dat
> RegMat: 
> -1.000  -0.012  -0.025  -0.000;
> -0.025   0.069   0.997   0.000;
>  0.010  -0.998   0.070  -0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
>  1.000   0.012   0.025   128.000;
> -0.010   0.998  -0.070   128.000;
> -0.025   0.069   0.997   128.000;
>  0.000   0.000   0.000   1.000;
> Allocating Hit Volume (16777216) voxels
> nlabels = 1
> Loading lh.words10_10.label
>
> Thesholding hit volume.
> Segmentation fault*
>
>
> I was surprised by this result, because it tells me that "the template
> voxel volume is 1". How strange! And finally, no nii file was generated.
>
> Can you help check whether I did something wrong? Attachment I put the
> files that might be used for running these two functions (I didn't put
> T1.mgz and rawavg.mgz in this email since it makes the file bigger
> than 500K, but if you need it please let

Re: [Freesurfer] A question as to subcortical volumetric measurement

[Douglas N Greve]

The FS segmentation is a combined segmentation and registration to an 
atlas space. This is probabilistic in that the atlas is built from 40 
subjects and uses intensity, location, and neighborhood priors. I think 
VBM is using unified segementation which performs intensity 
normalization, segmentation, and registration simultaneously also using 
a probabilistic atlas.  VBM segments GM/WM/CSF whereas FS segments 
various GM and ventricular structures as well as WM. VBM is a voxelwise 
analysis which is registered to an atlas, modulated, and spatially 
smoothed, all of which will have strong effects on the results. Maybe a 
VBM expert on the list can chime in with more info.

doug




On 11/05/2013 08:08 PM, jh kim wrote:
> Dear Drs. Bruce and Doug
> Thanks for the valuable comments.
>
> Discrepancy between FS and VBM lies in putamen and hippocampus.
> Would you please briefly comment regarding segmentation method of 
> above structures in FS?
> I'm just wondering whether segmentation of grey matter in FS is 
> largely different from that of VBM?
> Sorry for bothering you again with my silly question.
>
> Thanks.
> Kim
>
>
> 2013/11/5 Douglas N Greve  >
>
>
> Hi Kim, the answer is both easy and difficult. The easy answer is that
> they are completely different methods and will often give inconsistent
> results. I'm not sure what answer the reviewer will accept, and you
> might need to post the same question to the VBM and DARTEL crews. In
> your VBM analysis, I assume that you used modulation (ie, you were
> looking at volume and not "GM density")? VBM performs a voxel by voxel
> comparison and you probably smoothed by 10mm or so. Either of those
> could have washed out the effect. Certainly a reasonable response is
> that the FS analysis is for the entire ROI and and the VBM is
> voxelwise.
> Hope that help.s
>
> doug
>
>
>
> On 11/03/2013 11:55 PM, jh kim wrote:
> > Dear Doug and experts
> >
> > I've analyzed structural changes of the subcortical GM by using both
> > VBM (DARTEL in SPM8) and subcortical volumemetric measurement using
> > FreeSurfer 5.1. While there is no significant volumetric difference
> > between the groups in VBM (corrected p<0.05), FS results showed that
> > some subcortical GM had significant volume reductions in patients
> > relative to controls (MANCOVA controlling for the effect of ICV,
> age,
> > gender, followed by Bonferroni correction).
> > One of the referees raised the question regarding this discrepancy
> > between the VBM and FS findings.
> > How can I cope with it?
> >
> > Thank you in advance for your help.
> >
> > Kim
> >
> >
> > ___
> > 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.
>
>
>
>
> ___
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> 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
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Re: [Freesurfer] feat to qdec

[Christophe de Bezenac]

It was not in $FREESURFER_HOME/bin so I copied the  unix executable from 
the fsl/bin and pasted it into $FREESURFER_HOME/bin. It still fails at the 
flirt.fsl command?

Thanks,
Christophe 

  

On 6 Nov 2013, at 15:20, Douglas N Greve wrote:

> oops, sorry I just noticed that you did respond to the list!
> 
> On 11/06/2013 10:16 AM, Douglas N Greve wrote:
>> That should also be in $FREESURFER_HOME/bin. If not, just copy or
>> symlink your flirt program to it.
>> doug
>> 
>> ps. Please remember to post to the FS list and not to me personally. thanks!
>> 
>> 
>> 
>> On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
>>> Thanks for responding Doug,
>>> 
>>>  is in my path. I've actually now managed to run 
>>>  till the  command which produces the error 
>>> (Command not found).
>>> 
>>> /Users/chdebezenac
>>> flirt.fsl -ref 
>>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
>>>  -in 
>>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii
>>>  -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 
>>> -searchrz -90 90 -verbose 0 -omat 
>>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat
>>>  -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init 
>>> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat
>>> flirt.fsl: Command not found.
>>> ERROR: flirt
>>> 
>>> Do you know why this might be?
>>> 
>>> Thanks again,
>>> Christophe
>>> 
>>> 
>>> 
>>> On 5 Nov 2013, at 23:18, Douglas N Greve wrote:
>>> 
 Is reg-feat2anat in your path? It should be in
 $FREESURFER_HOME/bin/reg-feat2anat
 doug
 On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
> Hi everyone,
> 
> I am very new to freesurfer/qdec. What I would like to do is examine the 
> results of a feat analysis in qdec and then perform further 
> between-subject analyses with behavioural data 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). 
> I've run against problems at the first stage (registration) 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical).
>  I imagine something is not set up right?
> 
> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh
> setenv FREESURFER_HOME freesurfer
> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv 
> FREESURFER_HOME freesurfer
> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source 
> freesurfer/SetUpFreeSurfer.csh
>  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   freesurfer
> FSFAST_HOME   freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  freesurfer/subjects
> MNI_DIR   freesurfer/mni
> FSL_DIR   /usr/local/fsl
> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR 
> freesurferX/subjects
> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
> cd scan1Cor.feat
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
> chdebezenac% ln -s $SUBJECTS_DIR/fsaverage
> ln: ./fsaverage: File exists
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
> chdebezenac% ln -s $SUBJECTS_DIR/S1
> ln: ./S1: File exists
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
> chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
> reg-feat2anat: Command not found.
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat] 
> chdebezenac% cd
> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
> ls
> S1S4  fbert   lh.EC_average   
> scan1Cor.feat
> S2S5  fbert2.feat qdec
> S3bertfsaverage   rh.EC_average
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
> reg-feat2anat --feat scan1Cor.feat --subject S1
> reg-feat2anat: Command not found.
> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac%
> 
> Any help would be greatly appreciated,
> 
> Christophe
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> 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: 6

Re: [Freesurfer] glmfit for paired-diff on 2 groups

[Douglas N Greve]

Yes, that all looks correct. Though 25mm is a lot of smoothing. I 
usually use 10-15mm.
doug



On 11/06/2013 10:34 AM, Vivian R. Steiger wrote:
> Hi Doug
>
> Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in 
> the mailinglist
>
>
> Commands:
>
>
>   mris_preproc  --target 1_average_30VPs  --fsgd responder.txt  --hemi lh 
>  --meas thickness  --out respnon_lh_thickness.mgh —paired-diff-norm
>
>   mri_surf2surf --hemi lh --s 1_average_30VPs --fwhm 25 --sval 
> respnon_lh_thickness.mgh --cortex --tval respnon_lh_thickness.sm25.mgh
>
>   mri_glmfit  --y respnon_lh_thickness.sm25.mgh --fsgd 
> responder_paired.txt doss --C sad_groups.txt --surf 1_average_30VPs lh 
> --cortex --glmdir  respnon_lh_thickness
>
>
>
> FSGD 1: (responder.txt)
>
> GroupDescriptorFile 1
> Title Resonder_NonResponder
> Class resp
> Class nonresp
> Input 1Pre_VP02.long.VP02_Base resp
> Input 2Post_VP02.long.VP02_Base resp
> Input 1Pre_VP03.long.VP03_Base nonresp
> Input 2Post_VP03.long.VP03_Base nonresp
> Input 1Pre_VP04.long.VP04_Base resp
> Input 2Post_VP04.long.VP04_Base resp
> Input 1Pre_VP05.long.VP05_Base nonresp
> Input 2Post_VP05.long.VP05_Base nonresp
> Input 1Pre_VP06.long.VP06_Base resp
> Input 2Post_VP06.long.VP06_Base resp
> Input 1Pre_VP07.long.VP07_Base resp
> Input 2Post_VP07.long.VP07_Base resp
> Input 1Pre_VP08.long.VP08_Base resp
> Input 2Post_VP08.long.VP08_Base resp
> Input 1Pre_VP09.long.VP09_Base resp
> Input 2Post_VP09.long.VP09_Base resp
> Input 1Pre_VP10.long.VP10_Base nonresp
> Input 2Post_VP10.long.VP10_Base nonresp
> .
> .
> .
>
>
> FSGD 2: (responder_paired.txt)
>
> GroupDescriptorFile 1
> Class resp
> Class nonresp
> Input VP02pair resp
> Input VP03pair nonresp
> Input VP04pair resp
> Input VP05pair nonresp
> Input VP06pair resp
> Input VP07pair resp
> Input VP08pair resp
> Input VP09pair resp
> Input VP10pair nonresp
> .
> .
> .
>
>
> Best,
> Vivian
>
>
>
> _
> On 11/04/2013 03:34 PM, Douglas N Greve wrote:
>> Yes, that looks correct, though I could be more confident if you send
>> the command lines used and your fsgd file(s).
>> doug
>
> _
> On 10/31/2013 07:32 AM, Vivian R. Steiger wrote:
>> Dear FS-Experts,
>>
>> I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11))
>> with longitudinal data.
>> Participants from both groups had only 2 scan sessions in each case 10 weeks
>> apart.
>>
>> So far is used the glmfit-variant with --paired-diff option in the first
>> place. (based on
> http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> )
>> The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is
>> used in glm-fit for comparison with the contrast (1 -1) for group diffs.
>>
>> This approach confirmed our hypothesized effects but I'm not sure whether I
>> used the right strategy.
>>
>> Could you might help me with this issue?
>>
>> Thank in advance
>>
>>
>> Best,
>>
>> Vivian
>>
>>
>

-- 
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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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] feat to qdec

[Douglas N Greve]

did you copy it to "flirt.fsl"? Did you rehash afterwards?

On 11/06/2013 10:42 AM, Christophe de Bezenac wrote:
> It was not in $FREESURFER_HOME/bin so I copied the  unix executable 
> from the fsl/bin and pasted it into $FREESURFER_HOME/bin. It still fails at 
> the flirt.fsl command?
>
> Thanks,
> Christophe
>
>
>
> On 6 Nov 2013, at 15:20, Douglas N Greve wrote:
>
>> oops, sorry I just noticed that you did respond to the list!
>>
>> On 11/06/2013 10:16 AM, Douglas N Greve wrote:
>>> That should also be in $FREESURFER_HOME/bin. If not, just copy or
>>> symlink your flirt program to it.
>>> doug
>>>
>>> ps. Please remember to post to the FS list and not to me personally. thanks!
>>>
>>>
>>>
>>> On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
 Thanks for responding Doug,

  is in my path. I've actually now managed to run 
  till the  command which produces the error 
 (Command not found).

 /Users/chdebezenac
 flirt.fsl -ref 
 /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
  -in 
 /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii
  -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 
 -searchrz -90 90 -verbose 0 -omat 
 /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat
  -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init 
 /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat
 flirt.fsl: Command not found.
 ERROR: flirt

 Do you know why this might be?

 Thanks again,
 Christophe



 On 5 Nov 2013, at 23:18, Douglas N Greve wrote:

> Is reg-feat2anat in your path? It should be in
> $FREESURFER_HOME/bin/reg-feat2anat
> doug
> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
>> Hi everyone,
>>
>> I am very new to freesurfer/qdec. What I would like to do is examine the 
>> results of a feat analysis in qdec and then perform further 
>> between-subject analyses with behavioural data 
>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). 
>> I've run against problems at the first stage (registration) 
>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical).
>>  I imagine something is not set up right?
>>
>> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh
>> setenv FREESURFER_HOME freesurfer
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv 
>> FREESURFER_HOME freesurfer
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source 
>> freesurfer/SetUpFreeSurfer.csh
>>  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   freesurfer
>> FSFAST_HOME   freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  freesurfer/subjects
>> MNI_DIR   freesurfer/mni
>> FSL_DIR   /usr/local/fsl
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR 
>> freesurferX/subjects
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
>> cd scan1Cor.feat
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>  chdebezenac% ln -s $SUBJECTS_DIR/fsaverage
>> ln: ./fsaverage: File exists
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>  chdebezenac% ln -s $SUBJECTS_DIR/S1
>> ln: ./S1: File exists
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>  chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
>> reg-feat2anat: Command not found.
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>  chdebezenac% cd
>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
>> ls
>> S1   S4  fbert   lh.EC_average   
>> scan1Cor.feat
>> S2   S5  fbert2.feat qdec
>> S3   bertfsaverage   rh.EC_average
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac% 
>> reg-feat2anat --feat scan1Cor.feat --subject S1
>> reg-feat2anat: Command not found.
>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezenac%
>>
>> Any help would be greatly appreciated,
>>
>> Christophe
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FW: convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem

[Douglas N Greve]

OK, try this cmd

mri_vol2vol --mov $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --targ 
aseg.mgz --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz 
--inv --interp nearest


On 11/05/2013 06:49 PM, Roderick McColl wrote:
> Sure, no problem.
>
> Run from within the folder $SUBJECTS/fsaverage/mri :-
>
> mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov aseg.mgz 
> --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz
>
> mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov 
> aparc+aseg.mgz --reg transforms/reg.mni152.1mm.dat --o 
> aparc_aseg_mni152.nii.gz
>
> -roddy
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, November 05, 2013 5:21 PM
> To: Roderick McColl; Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into 
> $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
>
> Can you send your command lines for both aparc+aseg and aseg?
> doug
>
> ps. Please remember to post to the list and not to me personally. Thanks!
>
>
>
> On 11/05/2013 12:45 PM, Roderick McColl wrote:
>> Actually does not display properly at least not in freeview.
>> Slices are also upside down.
>> Also the output dims are 256x256x256 and I was expecting 182x218x182 which 
>> are the dims
>> For $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz.
>> But I agree that I should get in contact which the FSL people also.
>> Thanks
>> -roddy
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: Monday, November 04, 2013 5:22 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into 
>> $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
>>
>>
>> Hi Roddy, aparc+aseg.mgz and aseg.mgz are in the exact same space and the 
>> same command line should generate the same result. Does it display properly 
>> in tkmedit? If so and if you're having problems visualizing with fslview, 
>> contact the FSL crew.
>> doug
>>
>>
>>
>>
>> On 11/04/2013 05:52 PM, Roderick McColl wrote:
>>> Hmmm,
>>>
>>> Actually using aseg.mgz works just fine (just tried this now),
>>> displays correctly on fslview.
>>> What I was really trying to do was convert aparc+aseg.mgz which does
>>> not provide the expected orientation in fslview.
>>> Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow?
>>>
>>> For the aparc_aseg_mni152.nii.gz output,
>>> 1) the coronal image in fslview (top left)
>>>   has the S/I labels upside down compared to the coronal slice,
>>>   (or the coronal slice upside down compared to the S/I labels)
>>> 2) the sagittal image (top right) has the same S/I issue
>>> 3) the axial image (bottom left) has the A/P labels the
>>>   opposite of the image slice.
>>>
>>> Thanks for any advice
>>>
>>> -roddy
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Roderick McColl
>>> [roderick.mcc...@utsouthwestern.edu]
>>> Sent: Monday, November 04, 2013 3:37 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into
>>> $FSLDIR Nifti with MNI152_T1_1mm target
>>>
>>> I am obviously using mri_vol2vol incorrectly but I'm stumped.
>>>
>>> Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL 
>>> MNI152 space to do some fslmaths.
>>>
>>> >From looking around it seemed the command to accomplish this is
 (inside $SUBJECTS/fsaverage/mri)
>>> mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz  \
>>>--mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o
>>> asegmni152.nii.gz
>>>
>>> which does execute but if I load asegmni152.nii.gz into fslview all of the 
>>> orthogonal views are upside down.
>>>
>>> There is something missing regarding the co-ordinate system but I'm not 
>>> sure what.
>>>
>>> Can anyone point me in the right direction?
>>>
>>> Thanks
>>>
>>> -roddy
>>>
>>> 
>>>
>>> UT Southwestern Medical Center
>>> The future of medicine, today.
>>>
>>>
>>> ___
>>> 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.
>>>
>>>
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Re: [Freesurfer] glmfit for paired-diff on 2 groups

[Vivian R. Steiger]

hi doug

Thanks for checking my code and the hint with the smoothing rate. I appreciate 
your time on my issue.
I’ve ran a series of different smoothing rates (from 10-30mm) and 25mm showed 
the best results for our data in terms of cluster size but still prominent 
effects in summary statistics.

 vivian

Am 06.11.2013 um 16:43 schrieb Douglas N Greve :

> 
> Yes, that all looks correct. Though 25mm is a lot of smoothing. I usually use 
> 10-15mm.
> doug
> 
> 
> 
> On 11/06/2013 10:34 AM, Vivian R. Steiger wrote:
>> Hi Doug
>> 
>> Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in 
>> the mailinglist
>> 
>> 
>> Commands:
>> 
>> 
>>  mris_preproc  --target 1_average_30VPs  --fsgd responder.txt  --hemi lh 
>>  --meas thickness  --out respnon_lh_thickness.mgh —paired-diff-norm
>> 
>>  mri_surf2surf --hemi lh --s 1_average_30VPs --fwhm 25 --sval 
>> respnon_lh_thickness.mgh --cortex --tval respnon_lh_thickness.sm25.mgh
>> 
>>  mri_glmfit  --y respnon_lh_thickness.sm25.mgh --fsgd 
>> responder_paired.txt doss --C sad_groups.txt --surf 1_average_30VPs lh 
>> --cortex --glmdir  respnon_lh_thickness
>> 
>> 
>> 
>> FSGD 1: (responder.txt)
>> 
>> GroupDescriptorFile 1
>> Title Resonder_NonResponder
>> Class resp
>> Class nonresp
>> Input 1Pre_VP02.long.VP02_Base resp
>> Input 2Post_VP02.long.VP02_Base resp
>> Input 1Pre_VP03.long.VP03_Base nonresp
>> Input 2Post_VP03.long.VP03_Base nonresp
>> Input 1Pre_VP04.long.VP04_Base resp
>> Input 2Post_VP04.long.VP04_Base resp
>> Input 1Pre_VP05.long.VP05_Base nonresp
>> Input 2Post_VP05.long.VP05_Base nonresp
>> Input 1Pre_VP06.long.VP06_Base resp
>> Input 2Post_VP06.long.VP06_Base resp
>> Input 1Pre_VP07.long.VP07_Base resp
>> Input 2Post_VP07.long.VP07_Base resp
>> Input 1Pre_VP08.long.VP08_Base resp
>> Input 2Post_VP08.long.VP08_Base resp
>> Input 1Pre_VP09.long.VP09_Base resp
>> Input 2Post_VP09.long.VP09_Base resp
>> Input 1Pre_VP10.long.VP10_Base nonresp
>> Input 2Post_VP10.long.VP10_Base nonresp
>> .
>> .
>> .
>> 
>> 
>> FSGD 2: (responder_paired.txt)
>> 
>> GroupDescriptorFile 1
>> Class resp
>> Class nonresp
>> Input VP02pair resp
>> Input VP03pair nonresp
>> Input VP04pair resp
>> Input VP05pair nonresp
>> Input VP06pair resp
>> Input VP07pair resp
>> Input VP08pair resp
>> Input VP09pair resp
>> Input VP10pair nonresp
>> .
>> .
>> .
>> 
>> 
>> Best,
>> Vivian
>> 
>> 
>> 
>> _
>> On 11/04/2013 03:34 PM, Douglas N Greve wrote:
>>> Yes, that looks correct, though I could be more confident if you send
>>> the command lines used and your fsgd file(s).
>>> doug
>> 
>> _
>> On 10/31/2013 07:32 AM, Vivian R. Steiger wrote:
>>> Dear FS-Experts,
>>> 
>>> I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11))
>>> with longitudinal data.
>>> Participants from both groups had only 2 scan sessions in each case 10 weeks
>>> apart.
>>> 
>>> So far is used the glmfit-variant with --paired-diff option in the first
>>> place. (based on
>> http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
>> )
>>> The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is
>>> used in glm-fit for comparison with the contrast (1 -1) for group diffs.
>>> 
>>> This approach confirmed our hypothesized effects but I'm not sure whether I
>>> used the right strategy.
>>> 
>>> Could you might help me with this issue?
>>> 
>>> Thank in advance
>>> 
>>> 
>>> Best,
>>> 
>>> Vivian
>>> 
>>> 
>> 
> 
> -- 
> 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/
> 
> 
> 
> 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.
> 


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[Freesurfer] longitudinal hippocampal subfields

[Joana Braga Pereira]

Dear all,

I'm interested in assessing the changes in the volumes of hippocampal
subfields between 2 time points.

Can I use the longitudinal pipeline of Freesurfer and add the
-hippo-subfields flag to the longitudinal runs of the 2 time points?

Thanks!
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Re: [Freesurfer] feat to qdec

[Christophe de Bezenac]

Adding the .fsl extension to the flirt executable sorted it.

Many thanks,
Christophe




On 6 Nov 2013, at 15:45, Douglas N Greve wrote:

> did you copy it to "flirt.fsl"? Did you rehash afterwards?
> 
> On 11/06/2013 10:42 AM, Christophe de Bezenac wrote:
>> It was not in $FREESURFER_HOME/bin so I copied the  unix executable 
>> from the fsl/bin and pasted it into $FREESURFER_HOME/bin. It still fails at 
>> the flirt.fsl command?
>> 
>> Thanks,
>> Christophe
>> 
>>   
>> On 6 Nov 2013, at 15:20, Douglas N Greve wrote:
>> 
>>> oops, sorry I just noticed that you did respond to the list!
>>> 
>>> On 11/06/2013 10:16 AM, Douglas N Greve wrote:
 That should also be in $FREESURFER_HOME/bin. If not, just copy or
 symlink your flirt program to it.
 doug
 
 ps. Please remember to post to the FS list and not to me personally. 
 thanks!
 
 
 
 On 11/06/2013 05:11 AM, Christophe de Bezenac wrote:
> Thanks for responding Doug,
> 
>  is in my path. I've actually now managed to run 
>  till the  command which produces the error 
> (Command not found).
> 
> /Users/chdebezenac
> flirt.fsl -ref 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/refvol.fslregister.nii
>  -in 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/movvol.fslregister.nii
>  -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 
> -searchrz -90 90 -verbose 0 -omat 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/tmp/fslmat0.trans.mat
>  -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init 
> /Users/chdebezenac/fmridata/FirstLevel/S1/scan1/scan1Cor.feat/reg/freesurfer/exf2anat.init.fsl.mat
> flirt.fsl: Command not found.
> ERROR: flirt
> 
> Do you know why this might be?
> 
> Thanks again,
> Christophe
> 
> 
> 
> On 5 Nov 2013, at 23:18, Douglas N Greve wrote:
> 
>> Is reg-feat2anat in your path? It should be in
>> $FREESURFER_HOME/bin/reg-feat2anat
>> doug
>> On 11/05/2013 12:15 PM, Christophe de Bezenac wrote:
>>> Hi everyone,
>>> 
>>> I am very new to freesurfer/qdec. What I would like to do is examine 
>>> the results of a feat analysis in qdec and then perform further 
>>> between-subject analyses with behavioural data 
>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer).
>>>  I've run against problems at the first stage (registration) 
>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical).
>>>  I imagine something is not set up right?
>>> 
>>> Christophe-de-Bezenacs-MacBook-Pro:~ chdebezenac$ tcsh
>>> setenv FREESURFER_HOME freesurfer
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv 
>>> FREESURFER_HOME freesurfer
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% source 
>>> freesurfer/SetUpFreeSurfer.csh
>>>  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> FREESURFER_HOME   freesurfer
>>> FSFAST_HOME   freesurfer/fsfast
>>> FSF_OUTPUT_FORMAT nii.gz
>>> SUBJECTS_DIR  freesurfer/subjects
>>> MNI_DIR   freesurfer/mni
>>> FSL_DIR   /usr/local/fsl
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% setenv SUBJECTS_DIR 
>>> freesurferX/subjects
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] 
>>> chdebezenac% cd scan1Cor.feat
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>>  chdebezenac% ln -s $SUBJECTS_DIR/fsaverage
>>> ln: ./fsaverage: File exists
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>>  chdebezenac% ln -s $SUBJECTS_DIR/S1
>>> ln: ./S1: File exists
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>>  chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
>>> reg-feat2anat: Command not found.
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects/scan1Cor.feat]
>>>  chdebezenac% cd
>>> [Christophe-de-Bezenacs-MacBook-Pro:~] chdebezenac% cd $SUBJECTS_DIR
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] 
>>> chdebezenac% ls
>>> S1  S4  fbert   lh.EC_average   
>>> scan1Cor.feat
>>> S2  S5  fbert2.feat qdec
>>> S3  bertfsaverage   rh.EC_average
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] 
>>> chdebezenac% reg-feat2anat --feat scan1Cor.feat --subject S1
>>> reg-feat2anat: Command not found.
>>> [Christophe-de-Bezenacs-MacBook-Pro:~/freesurferX/subjects] chdebezena

Re: [Freesurfer] longitudinal hippocampal subfields

[Juan Eugenio Iglesias]

Dear Joana,
at this point, a "true" longitudinal version of the subfield 
segmentation is not available. However, we have noticed that you can get 
slightly better (more stable) results by segmenting the subfields in the 
longitudinally processed timepoints - rather than the original, 
cross-sectionally analyzed subjects that you used to create the base.

In other words: rather than running
recon-all -subjid tpN -hippo-subfields
you should run
recon-all -subjid tpN.long.base -hippo-subfields
Cheers,
Eugenio


On 11/06/2013 11:32 AM, Joana Braga Pereira wrote:

Dear all,

I'm interested in assessing the changes in the volumes of hippocampal 
subfields between 2 time points.


Can I use the longitudinal pipeline of Freesurfer and add the 
-hippo-subfields flag to the longitudinal runs of the 2 time points?


Thanks!


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--
-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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[Freesurfer] LME Mass Univariate analysis and .long directories

[Jonathan Holt]

FS experts,

I have two questions, when running mris_preproc and mri_surf2surf should I be 
passing these any of the .long directories created with recon-all -long? As I 
read through the tutorial I’m missing their significance in the analysis 
section of the longitudinal stream. It seems like fsaverage is being used (I’m 
not sure when that was even generated)

Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m 
wondering where, in your tutorial examples lh.thickness_sm10.mgh comes from/is 
located. Found in 

mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval 
lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape



best,

jon





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Re: [Freesurfer] longitudinal hippocampal subfields

[Joana Braga Pereira]

Great, thanks!


2013/11/6 Juan Eugenio Iglesias 

>  Dear Joana,
> at this point, a "true" longitudinal version of the subfield segmentation
> is not available. However, we have noticed that you can get slightly better
> (more stable) results by segmenting the subfields in the longitudinally
> processed timepoints - rather than the original, cross-sectionally analyzed
> subjects that you used to create the base.
> In other words: rather than running
> recon-all -subjid tpN -hippo-subfields
> you should run
> recon-all -subjid tpN.long.base -hippo-subfields
> Cheers,
> Eugenio
>
>
>
> On 11/06/2013 11:32 AM, Joana Braga Pereira wrote:
>
> Dear all,
>
>  I'm interested in assessing the changes in the volumes of hippocampal
> subfields between 2 time points.
>
>  Can I use the longitudinal pipeline of Freesurfer and add the
> -hippo-subfields flag to the longitudinal runs of the 2 time points?
>
>  Thanks!
>
>
> ___
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>
>
> --
> -
> Juan Eugenio Iglesias, 
> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>  The information in this e-mail is intended only for the person to whom
> it is
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> e-mail
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Re: [Freesurfer] LME Mass Univariate analysis and .long directories

[Martin Reuter]

Hi Jon,

passing the --qdec-long flag to mris_preproc will automatically generate the 
right names (e.g. the .long. directories) and take the data from there. You can 
pass the study_average vie the --target flag. The default is to use fsaverage 
which is distributed with FreeSurfer. 

So mris_preproc maps the thickness maps to the subject average, while the 
mris_surf2surf command is for smoothing the stack of thickness maps and 
generates the …_sm10.mgh file.

Best, Martin



On Nov 6, 2013, at 2:07 PM, Jonathan Holt  wrote:

> FS experts,
> 
> I have two questions, when running mris_preproc and mri_surf2surf should I be 
> passing these any of the .long directories created with recon-all -long? As I 
> read through the tutorial I’m missing their significance in the analysis 
> section of the longitudinal stream. It seems like fsaverage is being used 
> (I’m not sure when that was even generated)
> 
> Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m 
> wondering where, in your tutorial examples lh.thickness_sm10.mgh comes 
> from/is located. Found in 
> 
> mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval 
> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
> 
> 
> 
> best,
> 
> jon
> 
> 
> 
> 
> 
> ___
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-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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Re: [Freesurfer] longitudinal measures

[Martin Reuter]

Ups, sorry, missed your mail.

you can get the difference by two ways:

- you simply subtract the thickness maps in each subject by yourself and then 
use that for the analysis

- you put 0 and 1 into the longitudinal qdec table for the two time points. 
When the time distance is 1, the rate will be the difference.

Best, Martin

On Oct 24, 2013, at 4:30 PM, Qi Wu  wrote:

> Hi Freesurfer users,
> 
> For the longitudinal stream in FS5.1, there are only 4 options of measures 
> (do-avg, do-rate, do-pc1 and do-spc). However, if I need other measures, such 
> as the difference between two time points (thick2-thick1), how should I do to 
> get the values and still be able to do the voxel-wise analysis for regional 
> difference in cortical thickness (with glmfit)?
> 
> Many thanks
> 
> Keith
> Postdoc research fellow
> Toronto Western Hospital
> 
> The temporal average is simply the average thickness: avg = 0.5 * (thick1 + 
> thick2)
> The rate of change is the difference per time unit, so rate = ( thick2 - 
> thick1 ) / (time2 - time1). 
> The percent change (pc1) is the rate with respect to the thickness at the 
> first time point: pc1 = rate / thick1. 
> The symmetrized percent change (spc) is the rate with respect to the average 
> thickness: spc = rate / avg. 
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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Re: [Freesurfer] LME Mass Univariate analysis and .long directories

[Jonathan Holt]

Thanks a ton Martin,

can you possibly clue me into where I could find study_average?

best,
jon
On Nov 6, 2013, at 2:16 PM, Martin Reuter  wrote:

> Hi Jon,
> 
> passing the --qdec-long flag to mris_preproc will automatically generate the 
> right names (e.g. the .long. directories) and take the data from there. You 
> can pass the study_average vie the --target flag. The default is to use 
> fsaverage which is distributed with FreeSurfer. 
> 
> So mris_preproc maps the thickness maps to the subject average, while the 
> mris_surf2surf command is for smoothing the stack of thickness maps and 
> generates the …_sm10.mgh file.
> 
> Best, Martin
> 
> 
> 
> On Nov 6, 2013, at 2:07 PM, Jonathan Holt  wrote:
> 
>> FS experts,
>> 
>> I have two questions, when running mris_preproc and mri_surf2surf should I 
>> be passing these any of the .long directories created with recon-all -long? 
>> As I read through the tutorial I’m missing their significance in the 
>> analysis section of the longitudinal stream. It seems like fsaverage is 
>> being used (I’m not sure when that was even generated)
>> 
>> Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m 
>> wondering where, in your tutorial examples lh.thickness_sm10.mgh comes 
>> from/is located. Found in 
>> 
>> mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval 
>> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
>> 
>> 
>> 
>> best,
>> 
>> jon
>> 
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -
> Dr. Martin Reuter
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
> 
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
> 
> Phone: +1-617-724-5652
> Email: 
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu 
> 
> ___
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> 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.

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Re: [Freesurfer] longitudinal measures

[Qi Wu]

Thank you so much Martin. It is a very simple yet fantastic solution! Keith


On Wed, Nov 6, 2013 at 2:19 PM, Martin Reuter
wrote:

> Ups, sorry, missed your mail.
>
> you can get the difference by two ways:
>
> - you simply subtract the thickness maps in each subject by yourself and
> then use that for the analysis
>
> - you put 0 and 1 into the longitudinal qdec table for the two time
> points. When the time distance is 1, the rate will be the difference.
>
> Best, Martin
>
> On Oct 24, 2013, at 4:30 PM, Qi Wu  wrote:
>
> Hi Freesurfer users,
>
> For the longitudinal stream in FS5.1, there are only 4 options of measures
> (do-avg, do-rate, do-pc1 and do-spc). However, if I need other measures,
> such as the difference between two time points (thick2-thick1), how should
> I do to get the values and still be able to do the voxel-wise analysis for
> regional difference in cortical thickness (with glmfit)?
>
> Many thanks
>
> Keith
> Postdoc research fellow
> Toronto Western Hospital
>
>
>1. The temporal average is simply the average thickness: *avg = 0.5 *
>(thick1 + thick2)*
>2. The rate of change is the difference per time unit, so *rate = (
>thick2 - thick1 ) / (time2 - time1)*.
>3. The percent change (pc1) is the rate with respect to the thickness
>at the first time point: *pc1 = rate / thick1*.
>4. The symmetrized percent change (spc) is the rate with respect to
>the average thickness: *spc = rate / avg*.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> -
> Dr. Martin Reuter
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu
>
> 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.
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Re: [Freesurfer] LME Mass Univariate analysis and .long directories

[Martin Reuter]

Hi Jon,

that is just a placeholder, indicating that this can be your own average in a 
real study. You can simply use 'fsaverage' for it, now.

Best, Martin

On Nov 6, 2013, at 2:22 PM, Jonathan Holt  wrote:

> Thanks a ton Martin,
> 
> can you possibly clue me into where I could find study_average?
> 
> best,
> jon
> On Nov 6, 2013, at 2:16 PM, Martin Reuter  wrote:
> 
>> Hi Jon,
>> 
>> passing the --qdec-long flag to mris_preproc will automatically generate the 
>> right names (e.g. the .long. directories) and take the data from there. You 
>> can pass the study_average vie the --target flag. The default is to use 
>> fsaverage which is distributed with FreeSurfer. 
>> 
>> So mris_preproc maps the thickness maps to the subject average, while the 
>> mris_surf2surf command is for smoothing the stack of thickness maps and 
>> generates the …_sm10.mgh file.
>> 
>> Best, Martin
>> 
>> 
>> 
>> On Nov 6, 2013, at 2:07 PM, Jonathan Holt  wrote:
>> 
>>> FS experts,
>>> 
>>> I have two questions, when running mris_preproc and mri_surf2surf should I 
>>> be passing these any of the .long directories created with recon-all -long? 
>>> As I read through the tutorial I’m missing their significance in the 
>>> analysis section of the longitudinal stream. It seems like fsaverage is 
>>> being used (I’m not sure when that was even generated)
>>> 
>>> Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m 
>>> wondering where, in your tutorial examples lh.thickness_sm10.mgh comes 
>>> from/is located. Found in 
>>> 
>>> mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval 
>>> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
>>> 
>>> 
>>> 
>>> best,
>>> 
>>> jon
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> -
>> Dr. Martin Reuter
>> Assistant in Neuroscience - Massachusetts General Hospital
>> Instructor in Neurology   - Harvard Medical School
>> MGH / HMS / MIT
>> 
>> A.A.Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, MA 02129
>> 
>> Phone: +1-617-724-5652
>> Email: 
>>mreu...@nmr.mgh.harvard.edu
>>reu...@mit.edu
>> Web  : http://reuter.mit.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.
> 

-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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Re: [Freesurfer] LME Mass Univariate analysis and .long directories

[Jonathan Holt]

OH,

I see, then how would I generate my own study average, if I wanted to do so?


On Nov 6, 2013, at 2:48 PM, Martin Reuter  wrote:

> Hi Jon,
> 
> that is just a placeholder, indicating that this can be your own average in a 
> real study. You can simply use 'fsaverage' for it, now.
> 
> Best, Martin
> 
> On Nov 6, 2013, at 2:22 PM, Jonathan Holt  wrote:
> 
>> Thanks a ton Martin,
>> 
>> can you possibly clue me into where I could find study_average?
>> 
>> best,
>> jon
>> On Nov 6, 2013, at 2:16 PM, Martin Reuter  
>> wrote:
>> 
>>> Hi Jon,
>>> 
>>> passing the --qdec-long flag to mris_preproc will automatically generate 
>>> the right names (e.g. the .long. directories) and take the data from there. 
>>> You can pass the study_average vie the --target flag. The default is to use 
>>> fsaverage which is distributed with FreeSurfer. 
>>> 
>>> So mris_preproc maps the thickness maps to the subject average, while the 
>>> mris_surf2surf command is for smoothing the stack of thickness maps and 
>>> generates the …_sm10.mgh file.
>>> 
>>> Best, Martin
>>> 
>>> 
>>> 
>>> On Nov 6, 2013, at 2:07 PM, Jonathan Holt  wrote:
>>> 
 FS experts,
 
 I have two questions, when running mris_preproc and mri_surf2surf should I 
 be passing these any of the .long directories created with recon-all 
 -long? As I read through the tutorial I’m missing their significance in 
 the analysis section of the longitudinal stream. It seems like fsaverage 
 is being used (I’m not sure when that was even generated)
 
 Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m 
 wondering where, in your tutorial examples lh.thickness_sm10.mgh comes 
 from/is located. Found in 
 
 mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval 
 lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
 
 
 
 best,
 
 jon
 
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> -
>>> Dr. Martin Reuter
>>> Assistant in Neuroscience - Massachusetts General Hospital
>>> Instructor in Neurology   - Harvard Medical School
>>> MGH / HMS / MIT
>>> 
>>> A.A.Martinos Center for Biomedical Imaging
>>> 149 Thirteenth Street, Suite 2301
>>> Charlestown, MA 02129
>>> 
>>> Phone: +1-617-724-5652
>>> Email: 
>>>mreu...@nmr.mgh.harvard.edu
>>>reu...@mit.edu
>>> Web  : http://reuter.mit.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.
>> 
> 
> -
> Dr. Martin Reuter
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
> 
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
> 
> Phone: +1-617-724-5652
> Email: 
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu

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Re: [Freesurfer] LME Mass Univariate analysis and .long directories

[Martin Reuter]

Hi Jon,

Usually you would select a specific subject to be the target, sometimes 
that subject is in the mid age range, etc. Also sometimes people remove 
that subject from the study to not introduce a bias.


In most cases, however, people simply use fsaverage unless they have a 
reason to switch.


I don't know how you create your own 'average' surface. Maybe someone 
else can answer that.


Best, Martin


On 11/06/2013 02:57 PM, Jonathan Holt wrote:

OH,

I see, then how would I generate my own study average, if I wanted to 
do so?



On Nov 6, 2013, at 2:48 PM, Martin Reuter > wrote:



Hi Jon,

that is just a placeholder, indicating that this can be your own 
average in a real study. You can simply use 'fsaverage' for it, now.


Best, Martin

On Nov 6, 2013, at 2:22 PM, Jonathan Holt > wrote:



Thanks a ton Martin,

can you possibly clue me into where I could find study_average?

best,
jon
On Nov 6, 2013, at 2:16 PM, Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>> 
wrote:



Hi Jon,

passing the --qdec-long flag to mris_preproc will automatically 
generate the right names (e.g. the .long. directories) and take the 
data from there. You can pass the study_average vie the --target 
flag. The default is to use fsaverage which is distributed with 
FreeSurfer.


So mris_preproc maps the thickness maps to the subject average, 
while the mris_surf2surf command is for smoothing the stack of 
thickness maps and generates the …_sm10.mgh file.


Best, Martin



On Nov 6, 2013, at 2:07 PM, Jonathan Holt > wrote:



FS experts,

I have two questions, when running mris_preproc and mri_surf2surf 
should I be passing these any of the .long directories created 
with recon-all -long? As I read through the tutorial I’m missing 
their significance in the analysis section of the longitudinal 
stream. It seems like fsaverage is being used (I’m not sure when 
that was even generated)


Secondly, I see that mris_preproc outputs a thickness.mgh file, 
but I’m wondering where, in your tutorial examples 
lh.thickness_sm10.mgh comes from/is located. Found in


*mri_surf2surf* --hemi lh --s fsaverage --sval lh.thickness.mgh 
--tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape



best,

jon




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Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu 
reu...@mit.edu 
Web  : http://reuter.mit.edu 

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-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu 
reu...@mit.edu 
Web  : http://reuter.mit.edu 




--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] LME Mass Univariate analysis and .long directories

[Jonathan Holt]

Thank you Martin,

This is more than enough.

Jon
On Nov 6, 2013, at 3:42 PM, Martin Reuter  wrote:

> Hi Jon,
> 
> Usually you would select a specific subject to be the target, sometimes that 
> subject is in the mid age range, etc. Also sometimes people remove that 
> subject from the study to not introduce a bias.
> 
> In most cases, however, people simply use fsaverage unless they have a reason 
> to switch. 
> 
> I don't know how you create your own 'average' surface. Maybe someone else 
> can answer that.
> 
> Best, Martin
> 
> 
> On 11/06/2013 02:57 PM, Jonathan Holt wrote:
>> OH,
>> 
>> I see, then how would I generate my own study average, if I wanted to do so?
>> 
>> 
>> On Nov 6, 2013, at 2:48 PM, Martin Reuter  
>> wrote:
>> 
>>> Hi Jon,
>>> 
>>> that is just a placeholder, indicating that this can be your own average in 
>>> a real study. You can simply use 'fsaverage' for it, now.
>>> 
>>> Best, Martin
>>> 
>>> On Nov 6, 2013, at 2:22 PM, Jonathan Holt  wrote:
>>> 
 Thanks a ton Martin,
 
 can you possibly clue me into where I could find study_average?
 
 best,
 jon
 On Nov 6, 2013, at 2:16 PM, Martin Reuter  
 wrote:
 
> Hi Jon,
> 
> passing the --qdec-long flag to mris_preproc will automatically generate 
> the right names (e.g. the .long. directories) and take the data from 
> there. You can pass the study_average vie the --target flag. The default 
> is to use fsaverage which is distributed with FreeSurfer. 
> 
> So mris_preproc maps the thickness maps to the subject average, while the 
> mris_surf2surf command is for smoothing the stack of thickness maps and 
> generates the …_sm10.mgh file.
> 
> Best, Martin
> 
> 
> 
> On Nov 6, 2013, at 2:07 PM, Jonathan Holt  wrote:
> 
>> FS experts,
>> 
>> I have two questions, when running mris_preproc and mri_surf2surf should 
>> I be passing these any of the .long directories created with recon-all 
>> -long? As I read through the tutorial I’m missing their significance in 
>> the analysis section of the longitudinal stream. It seems like fsaverage 
>> is being used (I’m not sure when that was even generated)
>> 
>> Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m 
>> wondering where, in your tutorial examples lh.thickness_sm10.mgh comes 
>> from/is located. Found in 
>> 
>> mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval 
>> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
>> 
>> 
>> best,
>> 
>> jon
>> 
>> 
>> 
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -
> Dr. Martin Reuter
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
> 
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
> 
> Phone: +1-617-724-5652
> Email: 
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu 
> 
> ___
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> 
> 
> 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.
 
>>> 
>>> -
>>> Dr. Martin Reuter
>>> Assistant in Neuroscience - Massachusetts General Hospital
>>> Instructor in Neurology   - Harvard Medical School
>>> MGH / HMS / MIT
>>> 
>>> A.A.Martinos Center for Biomedical Imaging
>>> 149 Thirteenth Street, Suite 2301
>>> Charlestown, MA 02129
>>> 
>>> Phone: +1-617-724-5652
>>> Email: 
>>>mreu...@nmr.mgh.harvard.edu
>>>reu...@mit.edu
>>> Web  : http://reuter.mit.edu
>> 
> 
> -- 
> Martin Reuter, Ph.D.
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
> 
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
> 
> Phone: +1-617-724-5652
> Email: 
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu 
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> Freesurfer@nmr.mgh.harvard.

[Freesurfer] ltaReadFile error while running recon-all -long

[Jonathan Holt]

FS experts,

I’m having a bit of an issue with a single subject. Recon-all -long errors out 
after it tells me it cannot open the subjid_to_template.lta file. I’m very 
confused, because the file it’s looking for exists in the exact location it’s 
looking for but the recon-all.log suggests that there is no such file or 
directory. It proceeds to map control points and runs into a segmentation 
fault, after which it exits with errors. 

Any help would be appreciated.
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[Freesurfer] glm_fit --pvr

[celine]

Dear Freesurfer team
I am still trying to run a glm analysis between 2 surfaces but I am having
weird results so I guess I missed something.
So I sampled a DTI surface 2mm below the WM surface, and another
intracortical surface (T2* actually) at 75% depth from the pial surface.
The question I'd like to investigate is: is there a spatial relationship
between DTI metrics below the WM surface and intracortical metrics here
DTI in a patient population.
So I run glm_fit with -pvr option.
My design matrix has 2 classes (male and female) and 1 variable (age) that
I entered as covariates.
Here is the command:
mri_glmfit --y lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh
--pvr lh.L1_fsaverage_depth-2_fwhm5.mgh --fsgd ms_age_gender.fsgd --C
lh_age_gender_pvr.mtx --surf fsaverage lh --glmdir t20.75_L1-2

--y input is the T2* surfaces for each subject concatenated
-- pvr input is the DTI surface below the WM for each subject concatenated

I wasn't so sure about the contrast, as I have 2 class, 1 variable + the
pvr regressor I thought I would need 6 values (0 0 0 0 0 1) but I got an
error about the contrast saying I should put 5 factors so my contrast is 0
0 0 0 1, to test the slope between T2* and DTI at each vertex, after
taking into account gender and age.

The output sig.mgh doesn't give me any significant result, even at the
lowest possible threshold.

So my first question would be: is it fine to correlate different surfaces
that were not build at the same depth?
And the 2nd question would be: is the contrast correct to test the
correlation between the 2 surfaces at each vertex?

Thanks a lot for your help
Celine

PS: here is the terminal output:


gdfReadHeader: reading ms_age_gender.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 43.1176 9.02534
Class Means of each Continuous Variable
1 F  43.0435
2 M  43.2727
INFO: gd2mtx_method is dods
Reading source surface
/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.3/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd
/autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti
cmdline mri_glmfit --y
lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh --pvr
lh.L1_fsaverage_depth-2_fwhm5.mgh --fsgd ms_age_gender.fsgd --C
lh_age_gender_pvr.mtx --surf fsaverage lh --glmdir t20.75_L1-2
sysname  Linux
hostname panarea
machine  x86_64
user celine
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y   
/autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti/lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh
logyflag 0
usedti  0
FSGD ms_age_gender.fsgd
labelmask 
/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.3/fsaverage/label/lh.cortex.label
maskinv 0
glmdir t20.75_L1-2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory t20.75_L1-2
Loading y from
/autofs/cluster/mscat/users/sindhuja/data/3T/results_2013-11-06_t2star_dti/lh.t2star_corr_disco_fsaverage__r0.9_depth0.75_fwhm3.mgh
INFO: gd2mtx_method is dods
Saving design matrix to t20.75_L1-2/Xg.dat
Normalized matrix condition is 117.356
Matrix condition is 121295
Found 149955 points in label.
Pruning voxels by thr: 0.00
Found 2487 voxels in mask
Saving mask to t20.75_L1-2/mask.mgh
Reshaping mriglm->mask...
search space = 1064.228206
DOF = 29
Starting fit and test
Fit completed in 0.0014 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.602743, ar1std=0.415130, gstd=0.568767, fwhm=1.339345
Writing results
  lh_age_gender_pvr
maxvox sig=4.08  F=20.9043  at  index 63635 0 0seed=1384618381
mri_glmfit done

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[Freesurfer] unilateral hippocampus segmentation fail

[Andreas Berger]

Hi FreeSurfers,

i came across a few subjects in which FreeSurfer 5.3 failed to properly label 
most of the hippocampus in one hemisphere. Specifically, it is the left 
hippocampus in all of the 5 cases in which this occured. The subjects are 
young, healthy, and without any anatomical peculiarities. Segmentation was 
fine in these subjects with FreeSurfer 5.1.

Screenshots of one of these subjects are attached.

EDIT: that didn't seem to work, i uploaded them here:

http://www.students.meduniwien.ac.at/~n0642496/files/freesurfer/freeview_hippocampus_segmentation_fail_coronal.png
http://www.students.meduniwien.ac.at/~n0642496/files/freesurfer/freeview_hippocampus_segmentation_fail_sagittal.png


regards,
Andreas
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