Re: [Freesurfer] Cortical thickness values on a vertex base level

[Greve, Douglas N.,Ph.D.]

I'm not sure what you mean. Do you want the mean thickness of a cluster 
and/or its surface area?

On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
>
> External Email - Use Caution
>
> Dear developers,
>
> For a case-control study we are comparing the cortical thickness and 
> cortical surface area on a vertex-base level, for which we found 
> significant differences throughout the brain.
>
> Is it possible that, in addition to the significance values (p < .05 
> after FDR correction) on a vertex-base level, we can include the exact 
> thickness or surface area value (or difference) of the significant 
> clusters on a vertex base-level between the groups. In order words, to 
> provide some measures to highlight the size of the significant cluster 
> or the differences in cortical thickness / cortical surface area to 
> provide clinically useful context. For instance, a command comparable 
> to 'voxel size' in TBSS.
>
> As this is my first time using Freesurfer any help that you could 
> offer on this matter would be highly appreciated.
>
> Best wishes,
> Brigitte Dijkshoorn
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Fwd: Fw: glm error

[Amrita Bedi]

External Email - Use Caution

-- Forwarded message --
From: *abedi...@citymail.cuny.edu * <
abedi...@citymail.cuny.edu>
Date: Thursday, October 31, 2019
Subject: Fw: glm error
To: Amrita Bedi 




Amrita Bedi
*Biomedical Engineering - Class of 2018*
*The City College of New York - CUNY*

--
*From:* abedi...@citymail.cuny.edu
*Sent:* Thursday, October 31, 2019 12:02 PM
*To:* Freesurfer@nmr.mgh.harvard.edu 
*Subject:* glm error

Hello Freesurfer developers,

I ran a seed based resting stage functional analysis for 287 subjects using
the isthmus of the cingulate as a seed and now have pcc.nii.gz files in
each individual subject folder. I concatenated these pcc files and am
trying to run an osgm but get the following error:
ERROR: DOF = 0
The commands i ran for concatenating and glm are:
for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz
--i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done

 mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh
--cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi
/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir
all_subjects_lh_ic_pcc.TR3.glmdir

The mriglmfit.log gave me the following:


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
1to547_TR3/FSFAST
cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage
lh --cortex --label /run/media/amritabedilocal/
DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label
--glmdir all_subjects_lh_ic_pcc.TR3.glmdir
sysname  Linux
hostname imaging5.vaboston.lan
machine  x86_64
user root
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y/run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz
logyflag 0
usedti  0
labelmask  /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
1to547_TR3/fsaverage/label/lh.cortex.label
maskinv 0
glmdir all_subjects_lh_ic_pcc.TR3.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0

Thank you for your help.
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Re: [Freesurfer] Fwd: Fw: glm error

[Greve, Douglas N.,Ph.D.]

You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz  file correctly
Try
mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i 
*/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz

Where you have "bilat*", that should only be one folder


On 10/31/19 12:04 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
>
>
> -- Forwarded message --
> From: *abedi...@citymail.cuny.edu * 
> mailto:abedi...@citymail.cuny.edu>>
> Date: Thursday, October 31, 2019
> Subject: Fw: glm error
> To: Amrita Bedi mailto:amibedi...@gmail.com>>
>
>
>
>
> Amrita Bedi
> /Biomedical Engineering - Class of 2018/
> /The City College of New York - CUNY/
>
> 
> *From:* abedi...@citymail.cuny.edu 
> *Sent:* Thursday, October 31, 2019 12:02 PM
> *To:* Freesurfer@nmr.mgh.harvard.edu 
>  
> mailto:Freesurfer@nmr.mgh.harvard.edu>>
> *Subject:* glm error
> Hello Freesurfer developers,
>
> I ran a seed based resting stage functional analysis for 287 subjects 
> using the isthmus of the cingulate as a seed and now have pcc.nii.gz 
> files in each individual subject folder. I concatenated these pcc 
> files and am trying to run an osgm but get the following error:
> ERROR: DOF = 0
> The commands i ran for concatenating and glm are:
> for l in `cat sessidBOLD2`; do mri_concat --o 
> 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done
>
>  mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh 
> --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi
> /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir 
> all_subjects_lh_ic_pcc.TR3.glmdir
>
> The mriglmfit.log gave me the following:
>
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd 
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST
> cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf 
> fsaverage lh --cortex --label 
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label
>  
> --glmdir all_subjects_lh_ic_pcc.TR3.glmdir
> sysname  Linux
> hostname imaging5.vaboston.lan
> machine  x86_64
> user     root
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing     1
> OneSampleGroupMean 1
> y   
>  
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz
> logyflag 0
> usedti  0
> labelmask 
>  
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir all_subjects_lh_ic_pcc.TR3.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
>
> Thank you for your help.
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] nuisance factors

[Georgina Angelopoulou]

External Email - Use CautionDear Douglas, 

age_sim.mtx
Description: Binary data


CMTX_b.fsgd
Description: Binary data
Thank you once again for your reply and your help.Attached please find the fsgd file (CMTX_b.fsgd) including age row scores and the contrast file. The command line I used is the following:- mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdirThe output is the following:georgias-mbp:CMTX georgina$ mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdirgdfRead(): reading CMTX_b.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 age 45.2083 12.1603Class Means of each Continuous Variable1 patientmale  38.7778 2 patientfemale  53. 3 controlmale  40.1667 4 controlfemale  51.8462 INFO: gd2mtx_method is dodsReading source surface /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces    327680Total area         65416.984375AvgVtxArea       0.399269AvgVtxDist       0.721953StdVtxDist       0.195470$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $cwd /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTXcmdline mri_glmfit.bin --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir sysname  Darwinhostname 192.168.1.32machine  x86_64user     georginaFixVertexAreaFlag = 1UseMaskWithSmoothing     1OneSampleGroupMean 0y    /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mghlogyflag 0usedti  0FSGD CMTX_b.fsgdlabelmask  /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/label/lh.cortex.labelmaskinv 0glmdir lh.CMTX_b_thickness.glmdirIllCondOK 0ReScaleX 1DoFFx 0Creating output directory lh.CMTX_b_thickness.glmdirLoading y from /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh   ... done reading.INFO: gd2mtx_method is dodsSaving design matrix to lh.CMTX_b_thickness.glmdir/Xg.datComputing normalized matrixNormalized matrix condition is 160.248Matrix condition is 182721Found 149955 points in label.Pruning voxels by thr: 1.175494e-38Found 148239 voxels in maskSaving mask to lh.CMTX_b_thickness.glmdir/mask.mghReshaping mriglm->mask...search space = 73702.448371ERROR: dimension mismatch between X and contrast Contrasts/age_sim.mtx       X has 8 cols, C has 5 colsPlease note that an equivalent error appears with grey matter volume and surface area. Thank you once again,Best, Georgina___
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Re: [Freesurfer] FSGD file formatting for Xhemi

[Jose Graterol]

External Email - Use Caution

My doubt is, if it is possible to use a FSGD file to add variables to a
--paired-diff analysis. If it is, what would be the right way to format the
FSGD file.

Thanks in advance.

On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't understand. What per hemisphere variable?
>
> On 10/25/2019 3:15 AM, Jose Graterol wrote:
>
> External Email - Use Caution
> Thanks for your answer. A follow up question:
> How should I then specify the variable's values per hemisphere
> while making the FSGD file if I want to add covariates when
> running mri_glmfit?
>
> Thanks in advance.
>
> On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> If you are trying to determine whether the hemispheres are different,
>> then you need to do the subtraction between the hemis (ie, the
>> --paired-diff). If you want to look at the hemispheres separately, then
>> don't combine them in a single file
>>
>> On 10/21/19 4:58 AM, Jose Graterol wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for your answer.
>> >
>> > I want to correlate TMS values in 17 stroke patients. Following the
>> > instructions provided to Anders in this link
>> >
>> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1
>> > I created the --y file that joins the affected hemispheres together
>> > and the unaffected hemispheres together. I omitted the --paired-diff
>> > flag. When I run mri_glmfit with --fsgd it asks for 34 inputs. I am
>> > guessing those are for the 34 hemispheres of the patients in the order
>> > mentioned in my first email. Would this be the right way to correlate
>> > the variables?
>> >
>> > In short, I am trying to test if there is a difference in cortical
>> > thickness, while adding covariates, between the affected and
>> > unaffected hemispheres in stroke patients.
>> >
>> > Thanks in advance
>> >
>> > On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > What are you trying to test? Usually you don't have lh and rh in
>> > the same glm
>> >
>> > On 10/17/19 7:09 AM, Jose Graterol wrote:
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Dear Freesurfer Community,
>> >>
>> >> I have a question regarding the formatting of the FSGD file while
>> >> doing an analysis with Xhemi.
>> >> First the --y file was created as previously explained in another
>> >> discussion
>> >> (
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html
>> ).
>> >> That is, mris_preproc with --xhemi and no --fsgd flag.
>> >>
>> >> If I understood correctly, that would create a mgh file with the
>> >> following order: sub01lh, sub01rh, sub02lh, sub02rh...
>> >> Then the FSGD file while running mri_glmfit would be:
>> >> GroupDescriptorFile 1
>> >> Title xxx
>> >> Class sub
>> >> Variables   var1
>> >> Input   sub01lh   sub   var1_lh_sub01
>> >> Input   sub01rh   sub   var1_rh_sub01
>> >> Input   sub02lh   sub   var1_lh_sub02
>> >> Input   sub02rh   sub   var1_rh_sub02
>> >>
>> >> Would this be correct? If so, what would be the best case for
>> >> specifying a variable like age? Just repeating the value 2 times?
>> >>
>> >> As always, thanks in advance
>> >>
>> >> Kind Regards
>> >>
>> >> José
>> >>
>> >>
>> >> ___
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>> >> Freesurfer@nmr.mgh.harvard.edu  > Freesurfer@nmr.mgh.harvard.edu>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > ___
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>> > 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
>>
>>
>> ___
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>
>
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>
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[Freesurfer] PETsurfer issue

[Mackenzie Leigh Carlson]

External Email - Use Caution

Hello,

Wondering if anyone has had issues with PETsurfer partial volume correction.  
When I have used it, there are large 'holes' in the white matter. I am mostly 
interested in the hippocampal area, which seems unaffected by these holes, but 
I'm not sure if I should trust the outcome enough to still use PVC maps for the 
hippocampus! Any help is appreciated. Thank you!

I am running this:
mri_gtmpvc --i SUV-30-60-float-FixedSlope.nii.gz --reg SUVtoFS.reg.lta --psf 5 
--seg gtmseg.mgz  --default-seg-merge  --auto-mask PSF .01 --mgx .01 --o 
gtmpvc.output.nopons --no-rescale


--
Mackenzie L. Carlson
PhD Candidate in Bioengineering | Stanford University
BA Engineering Sciences | Dartmouth College
(218) 269-7473
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Re: [Freesurfer] Cortical thickness values on a vertex base level

[Aicha Dijkshoorn]

External Email - Use Caution

Dear Greve,

Thank you for your quick respons.

Yes, I believe that is what I mean. Let me illustrate with some (fictive) data;
We were able to prove these data for the entire hemisphere as can be seen below.






Group 1

Group 2

Difference

Sig.

Thickness

(in mm)

Left

1.48

1.46

.004

.19

Right

1.46

1.46

.003

.03





However, we would like to provide similar data in our vertex-base analyses:

Significantly different clusters between group 1 and group 2

Cortical thickness group 1

Cortical thickness group 2

Difference in mm2

Sig.

Left Cuneus

?

?

?

0.013

Left Fusiform gyrus

?

?

?

0.021

Right Paracentral lobule

?

?

?

0.001

Right parahippocampal gyrus

?

?

?

0.002

Does this clarify my question?

Best wishes,
Aicha




Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 namens Greve, Douglas N.,Ph.D. 

Verzonden: donderdag 31 oktober 2019 16:25
Aan: freesurfer@nmr.mgh.harvard.edu 
Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level

I'm not sure what you mean. Do you want the mean thickness of a cluster
and/or its surface area?

On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
>
> External Email - Use Caution
>
> Dear developers,
>
> For a case-control study we are comparing the cortical thickness and
> cortical surface area on a vertex-base level, for which we found
> significant differences throughout the brain.
>
> Is it possible that, in addition to the significance values (p < .05
> after FDR correction) on a vertex-base level, we can include the exact
> thickness or surface area value (or difference) of the significant
> clusters on a vertex base-level between the groups. In order words, to
> provide some measures to highlight the size of the significant cluster
> or the differences in cortical thickness / cortical surface area to
> provide clinically useful context. For instance, a command comparable
> to 'voxel size' in TBSS.
>
> As this is my first time using Freesurfer any help that you could
> offer on this matter would be highly appreciated.
>
> Best wishes,
> Brigitte Dijkshoorn
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] FSGD file formatting for Xhemi

[Greve, Douglas N.,Ph.D.]

There are not any restrictions, just do the same as you would for a 
non-paired analysis. In any event, you are creating a linear model
y = a +b1*x1 + b2*x2 ...
where y is the input (paired diff) and x1, x2, etc, are your factors. 
You are the one who knows your data and what models would be appropriate

On 10/31/19 12:41 PM, Jose Graterol wrote:
>
> External Email - Use Caution
>
> My doubt is, if it is possible to use a FSGD file to add variables to 
> a --paired-diff analysis. If it is, what would be the right way to 
> format the FSGD file.
>
> Thanks in advance.
>
> On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I don't understand. What per hemisphere variable?
>
> On 10/25/2019 3:15 AM, Jose Graterol wrote:
>>
>> External Email - Use Caution
>>
>> Thanks for your answer. A follow up question:
>> How should I then specify the variable's values per hemisphere
>> while making the FSGD file if I want to add covariates when
>> running mri_glmfit?
>>
>> Thanks in advance.
>>
>> On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>
>> If you are trying to determine whether the hemispheres are
>> different,
>> then you need to do the subtraction between the hemis (ie, the
>> --paired-diff). If you want to look at the hemispheres
>> separately, then
>> don't combine them in a single file
>>
>> On 10/21/19 4:58 AM, Jose Graterol wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for your answer.
>> >
>> > I want to correlate TMS values in 17 stroke patients.
>> Following the
>> > instructions provided to Anders in this link
>> >
>> 
>> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1
>>
>> > I created the --y file that joins the affected hemispheres
>> together
>> > and the unaffected hemispheres together. I omitted the
>> --paired-diff
>> > flag. When I run mri_glmfit with --fsgd it asks for 34
>> inputs. I am
>> > guessing those are for the 34 hemispheres of the patients
>> in the order
>> > mentioned in my first email. Would this be the right way to
>> correlate
>> > the variables?
>> >
>> > In short, I am trying to test if there is a difference in
>> cortical
>> > thickness, while adding covariates, between the affected and
>> > unaffected hemispheres in stroke patients.
>> >
>> > Thanks in advance
>> >
>> > On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>
>> > >> wrote:
>> >
>> >     What are you trying to test? Usually you don't have lh
>> and rh in
>> >     the same glm
>> >
>> >     On 10/17/19 7:09 AM, Jose Graterol wrote:
>> >>
>> >>     External Email - Use Caution
>> >>
>> >>     Dear Freesurfer Community,
>> >>
>> >>     I have a question regarding the formatting of the FSGD
>> file while
>> >>     doing an analysis with Xhemi.
>> >>     First the --y file was created as previously explained
>> in another
>> >>     discussion
>> >>   
>>  
>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html).
>> >>     That is, mris_preproc with --xhemi and no --fsgd flag.
>> >>
>> >>     If I understood correctly, that would create a mgh
>> file with the
>> >>     following order: sub01lh, sub01rh, sub02lh, sub02rh...
>> >>     Then the FSGD file while running mri_glmfit would be:
>> >>     GroupDescriptorFile 1
>> >>     Title xxx
>> >>     Class sub
>> >>     Variables   var1
>> >>     Input   sub01lh   sub   var1_lh_sub01
>> >>     Input   sub01rh   sub   var1_rh_sub01
>> >>     Input   sub02lh   sub   var1_lh_sub02
>> >>     Input   sub02rh   sub   var1_rh_sub02
>> >>
>> >>     Would this be correct? If so, what would be the best
>> case for
>> >>     specifying a variable like age? Just repeating the
>> value 2 times?
>> >>
>> >>     As always, thanks in advance
>> >>
>> >>     Kind Regards
>> >>
>> >>     José
>> >>
>> >>
>> >>  ___
>> >>     Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> 
>>  

Re: [Freesurfer] PETsurfer issue

[Greve, Douglas N.,Ph.D.]

The MGX method is only valid in voxels that have some gray matter in 
them (defined as 1% in the command line below), so any WM is set to 0 
(probably accounts for the big hole that you see). The mgx output is 
divided into cortical GM and subcortical GM, so you are probably looking 
at the cortical GM part.

On 10/31/19 1:12 PM, Mackenzie Leigh Carlson wrote:
>
> External Email - Use Caution
>
> Hello,
>
> Wondering if anyone has had issues with PETsurfer partial volume 
> correction.  When I have used it, there are large 'holes' in the white 
> matter. I am mostly interested in the hippocampal area, which seems 
> unaffected by these holes, but I'm not sure if I should trust the 
> outcome enough to still use PVC maps for the hippocampus! Any help is 
> appreciated. Thank you!
>
> I am running this:
> mri_gtmpvc --i SUV-30-60-float-FixedSlope.nii.gz --reg SUVtoFS.reg.lta 
> --psf 5 --seg gtmseg.mgz  --default-seg-merge  --auto-mask PSF .01 
> --mgx .01 --o gtmpvc.output.nopons --no-rescale
>
>
> --
> Mackenzie L. Carlson
> PhD Candidate in Bioengineering | Stanford University
> BA Engineering Sciences | Dartmouth College
> (218) 269-7473
>
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Re: [Freesurfer] Cortical thickness values on a vertex base level

[Greve, Douglas N.,Ph.D.]

You can run mri_surfcluster with your fdr threshold as the --thmin 
value. This will output cluster number (ocn) map. This will assign the 
cluster number to a vertex. You can then use mri_segstats with --seg 
ocn.mgz --excludeid 0 and input being the mean thickness or area maps. 
When you use area as thhe input, make sure to --accumulate to get the 
total area. You can get an area map in the same way that you got the 
thickness map, ie, mris_preproc, etc

On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
>
> External Email - Use Caution
>
> Dear Greve,
>
> Thank you for your quick respons.
>
> Yes, I believe that is what I mean. Let me illustrate with some 
> (fictive) data;
> We were able to prove these data for the entire hemisphere as can be 
> seen below.
>
>   
>
>   
>
> *Group 1*
>
>   
>
> *Group 2*
>
>   
>
> *Difference*
>
>   
>
> */Sig./*
>
> Thickness
>
> (in mm)
>
>   
>
> Left
>
>   
>
> 1.48
>
>   
>
> 1.46
>
>   
>
> .004
>
>   
>
> .19
>
> Right
>
>   
>
> 1.46
>
>   
>
> 1.46
>
>   
>
> .003
>
>   
>
> .03
>
>
>
>
>
>
> However, we would like to provide similar data in our vertex-base 
> analyses:
>
> *Significantly different clusters between group 1 and group 2*
>
>   
>
> *Cortical thickness group 1*
>
>   
>
> *Cortical thickness group 2*
>
>   
>
> *Difference in mm2*
>
>   
>
> */Sig./*
>
> Left Cuneus
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> 0.013
>
> Left Fusiform gyrus
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> 0.021
>
> Right Paracentral lobule
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> 0.001
>
> Right parahippocampal gyrus
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> ?
>
>   
>
> 0.002
>
>
> Does this clarify my question?
>
> Best wishes,
> Aicha
>
>
>
> 
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  namens Greve, Douglas 
> N.,Ph.D. 
> *Verzonden:* donderdag 31 oktober 2019 16:25
> *Aan:* freesurfer@nmr.mgh.harvard.edu 
> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex 
> base level
> I'm not sure what you mean. Do you want the mean thickness of a cluster
> and/or its surface area?
>
> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
> >
> > External Email - Use Caution
> >
> > Dear developers,
> >
> > For a case-control study we are comparing the cortical thickness and
> > cortical surface area on a vertex-base level, for which we found
> > significant differences throughout the brain.
> >
> > Is it possible that, in addition to the significance values (p < .05
> > after FDR correction) on a vertex-base level, we can include the exact
> > thickness or surface area value (or difference) of the significant
> > clusters on a vertex base-level between the groups. In order words, to
> > provide some measures to highlight the size of the significant cluster
> > or the differences in cortical thickness / cortical surface area to
> > provide clinically useful context. For instance, a command comparable
> > to 'voxel size' in TBSS.
> >
> > As this is my first time using Freesurfer any help that you could
> > offer on this matter would be highly appreciated.
> >
> > Best wishes,
> > Brigitte Dijkshoorn
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] nuisance factors

[Greve, Douglas N.,Ph.D.]

You have to specify that this is a DOSS analysis with

--fsgd CMTX_b.fsgd doss


On 10/31/19 12:38 PM, Georgina Angelopoulou wrote:
>
> External Email - Use Caution
>
> Dear Douglas,
>
> Thank you once again for your reply and your help.
>
> Attached please find the fsgd file (CMTX_b.fsgd) including age row 
> scores and the contrast file. The command line I used is the following:
> - mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C 
> Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir 
> lh.CMTX_b_thickness.glmdir
>
> The output is the following:
>
> georgias-mbp:CMTX georgina$ mri_glmfit --y lh.CMTX_b.thickness.10.mgh 
> --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh 
> --cortex --glmdir lh.CMTX_b_thickness.glmdir
> gdfRead(): reading CMTX_b.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 age 45.2083 12.1603
> Class Means of each Continuous Variable
> 1 patientmale  38.7778
> 2 patientfemale  53.
> 3 controlmale  40.1667
> 4 controlfemale  51.8462
> INFO: gd2mtx_method is dods
> Reading source surface 
> /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/surf/lh.white
> Number of vertices 163842
> Number of faces    327680
> Total area         65416.984375
> AvgVtxArea       0.399269
> AvgVtxDist       0.721953
> StdVtxDist       0.195470
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> cwd /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX
> cmdline mri_glmfit.bin --y lh.CMTX_b.thickness.10.mgh --fsgd 
> CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex 
> --glmdir lh.CMTX_b_thickness.glmdir
> sysname Darwin
> hostname 192.168.1.32
> machine x86_64
> user   georgina
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing     1
> OneSampleGroupMean 0
> y 
> /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh
> logyflag 0
> usedti 0
> FSGD CMTX_b.fsgd
> labelmask 
> /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir lh.CMTX_b_thickness.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory lh.CMTX_b_thickness.glmdir
> Loading y from 
> /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh
>    ... done reading.
> INFO: gd2mtx_method is dods
> Saving design matrix to lh.CMTX_b_thickness.glmdir/Xg.dat
> Computing normalized matrix
> Normalized matrix condition is 160.248
> Matrix condition is 182721
> Found 149955 points in label.
> Pruning voxels by thr: 1.175494e-38
> Found 148239 voxels in mask
> Saving mask to lh.CMTX_b_thickness.glmdir/mask.mgh
> Reshaping mriglm->mask...
> search space = 73702.448371
> ERROR: dimension mismatch between X and contrast Contrasts/age_sim.mtx 
>       X has 8 cols, C has 5 cols
>
>
> Please note that an equivalent error appears with grey matter volume 
> and surface area.
> Thank you once again,
>
> Best,
> Georgina


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Re: [Freesurfer] Fw: glm error

[Amrita Bedi]

External Email - Use Caution

Thank you Dr Greve, that issue is resolved.

I do have another question. I’m now trying to extract mean correlation
values to the seed from each individual subject and not sure how to go
about this.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz  file correctly
> Try
> mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i
> */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz
>
> Where you have "bilat*", that should only be one folder
>
>
> On 10/31/19 12:04 PM, Amrita Bedi wrote:
> >
> > External Email - Use Caution
> >
> >
> >
> > -- Forwarded message --
> > From: *abedi...@citymail.cuny.edu *
> > mailto:abedi...@citymail.cuny.edu>>
> > Date: Thursday, October 31, 2019
> > Subject: Fw: glm error
> > To: Amrita Bedi mailto:amibedi...@gmail.com>>
> >
> >
> >
> >
> > Amrita Bedi
> > /Biomedical Engineering - Class of 2018/
> > /The City College of New York - CUNY/
> >
> > 
> > *From:* abedi...@citymail.cuny.edu 
> > *Sent:* Thursday, October 31, 2019 12:02 PM
> > *To:* Freesurfer@nmr.mgh.harvard.edu
> > 
> > mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > *Subject:* glm error
> > Hello Freesurfer developers,
> >
> > I ran a seed based resting stage functional analysis for 287 subjects
> > using the isthmus of the cingulate as a seed and now have pcc.nii.gz
> > files in each individual subject folder. I concatenated these pcc
> > files and am trying to run an osgm but get the following error:
> > ERROR: DOF = 0
> > The commands i ran for concatenating and glm are:
> > for l in `cat sessidBOLD2`; do mri_concat --o
> > 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz;
> done
> >
> >  mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh
> > --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi
> > /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir
> > all_subjects_lh_ic_pcc.TR3.glmdir
> >
> > The mriglmfit.log gave me the following:
> >
> >
> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> > cwd
> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
> 1to547_TR3/FSFAST
> > cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf
> > fsaverage lh --cortex --label
> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
> 1to547_TR3/fsaverage/label/lh.cortex.label
> > --glmdir all_subjects_lh_ic_pcc.TR3.glmdir
> > sysname  Linux
> > hostname imaging5.vaboston.lan
> > machine  x86_64
> > user root
> > FixVertexAreaFlag = 1
> > UseMaskWithSmoothing 1
> > OneSampleGroupMean 1
> > y
> >  /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
> 1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz
> > logyflag 0
> > usedti  0
> > labelmask
> >  /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_
> 1to547_TR3/fsaverage/label/lh.cortex.label
> > maskinv 0
> > glmdir all_subjects_lh_ic_pcc.TR3.glmdir
> > IllCondOK 0
> > ReScaleX 1
> > DoFFx 0
> >
> > Thank you for your help.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Fw: glm error

[Greve, Douglas N.,Ph.D.]

mean over what? a parcellation? an activation cluster?

On 10/31/2019 3:15 PM, Amrita Bedi wrote:

External Email - Use Caution

Thank you Dr Greve, that issue is resolved.

I do have another question. I’m now trying to extract mean correlation values 
to the seed from each individual subject and not sure how to go about this.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz  file correctly
Try
mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i
*/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz

Where you have "bilat*", that should only be one folder


On 10/31/19 12:04 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
>
>
> -- Forwarded message --
> From: *abedi...@citymail.cuny.edu 
> >*
> mailto:abedi...@citymail.cuny.edu> 
> >>
> Date: Thursday, October 31, 2019
> Subject: Fw: glm error
> To: Amrita Bedi mailto:amibedi...@gmail.com> 
> >>
>
>
>
>
> Amrita Bedi
> /Biomedical Engineering - Class of 2018/
> /The City College of New York - CUNY/
>
> 
> *From:* abedi...@citymail.cuny.edu 
> >
> *Sent:* Thursday, October 31, 2019 12:02 PM
> *To:* Freesurfer@nmr.mgh.harvard.edu
> >
> mailto:Freesurfer@nmr.mgh.harvard.edu> 
> >>
> *Subject:* glm error
> Hello Freesurfer developers,
>
> I ran a seed based resting stage functional analysis for 287 subjects
> using the isthmus of the cingulate as a seed and now have pcc.nii.gz
> files in each individual subject folder. I concatenated these pcc
> files and am trying to run an osgm but get the following error:
> ERROR: DOF = 0
> The commands i ran for concatenating and glm are:
> for l in `cat sessidBOLD2`; do mri_concat --o
> 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done
>
>  mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh
> --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi
> /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir
> all_subjects_lh_ic_pcc.TR3.glmdir
>
> The mriglmfit.log gave me the following:
>
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST
> cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf
> fsaverage lh --cortex --label
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label
> --glmdir all_subjects_lh_ic_pcc.TR3.glmdir
> sysname  Linux
> hostname imaging5.vaboston.lan
> machine  x86_64
> user root
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 1
> y
>  
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz
> logyflag 0
> usedti  0
> labelmask
>  
> /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir all_subjects_lh_ic_pcc.TR3.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
>
> Thank you for your help.
>
>
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Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

[Bronwyn Overs]

External Email - Use Caution

Hi Kersten, 

Thanks you so much for your reply and sorry I missed your earlier message. I'll 
implement the suggestions you've suggested. Thanks again. 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



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From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Tuesday, October 29, 2019 9:21:59 PM 
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels 



External Email - Use Caution 


Hm, 

I think I replied last Wednesday; anyway, below is the message again. 

Best regards, 

Kersten 

 Forwarded Message  
From : "Diers, Kersten /DZNE" < [ 
mailto:%22Diers,%20Kersten%20/dzne%22%20%3ckersten.di...@dzne.de%3e | 
kersten.di...@dzne.de ] > 
Reply-to: Freesurfer support list  
To : freesurfer@nmr.mgh.harvard.edu < [ 
mailto:%22freesur...@nmr.mgh.harvard.edu%22%20%3cfreesur...@nmr.mgh.harvard.edu%3e
 | freesurfer@nmr.mgh.harvard.edu ] > 
Subject : Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels 
Date : Wed, 23 Oct 2019 07:39:54 + 



External Email - Use Caution 


Hi Bronwyn, 

thanks for sending the files. 

I've taken a look, and suggest that you leave out the '--thmax 5' argument from 
your mri_surfcluster command. Then, it may still be necessary to set the label 
threshold value in Freeview to a value below zero. 

When I run the modified mri_surfcluster command with the example data you 
provided, the created label resembled the mgh file, i.e. no cut-outs in regions 
of high significance were present. 

Best regards, 

Kersten 


On Di, 2019-10-29 at 16:46 +1100, Bronwyn Overs wrote: 




External Email - Use Caution 


Hi Kersten, 

Did you recieve the files I dropped to [ mailto:mreu...@nmr.mgh.harvard.edu | 
mreu...@nmr.mgh.harvard.edu ] on the 16th of October (titled 
'BAR_Sydney_FSIssues_SurfThreshLabels.zip')? 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



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From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Wednesday, October 16, 2019 2:15:53 AM 
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels 



External Email - Use Caution 


Hi, 

please use [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] 
, he'll forward it to me. 

Thanks, 

Kersten 


On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote: 

BQ_BEGIN


External Email - Use Caution 


Hi Kersten, 

That would be very helpful thank you. What email address should I designate as 
the recipient when using Freesurfer FileDrop? 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


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From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Wednesday, October 2, 2019 4:21:32 PM 
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster 
labels 



External Email - Use Caution 


Hi Bronwyn, 

thanks for the update and additional info. 

I have to say that I have no very good clue at the moment. 

Could you maybe upload an examplary file to the Freesurfer FileDrop at [ 
https://gate.nmr.mgh.harvard.edu/filedrop2/ | 
https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer 
look? 

Best regards, 

Kersten 


On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote: 

BQ_BEGIN


External Email - Use Caution 


Hi Kersten, 

Thank you for your detailed reply and sorry for this delayed response. 

Yes the top row in my figure (attached again) was produced by using the 
'--olab' argument with the 'mri_surfcluster' command and then loading each 
cluster from a different label file. I attempted to follow your suggestion and 
adjust the label 'threshold' in Freeview to minimum value in my significance 
map (-5), but this did not display the missing regions - the surface remained 
the same as row 1 of the attached figure. 

To prov

Re: [Freesurfer] make_average_subject error

[Maxime Perron]

External Email - Use Caution
Hi Andrew,


I am very sorry for the delay of my answer. 


Everything works with the patch. 


Thank you so much!


Cheers,
Maxime


On Oct 10, 2019, at 11:39 AM, Hoopes, Andrew  wrote:




Hi Maxine,

 

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ contains
 executables and a README file that details how you can patch your freesurfer install to fix this issue.

 

best

Andrew

 

 


From: 
 on behalf of Maxime Perron 
Reply-To: FS Help 
Date: Friday, September 6, 2019 at 5:08 PM
To: FS Help 
Subject: Re: [Freesurfer] make_average_subject error



 

External Email - Use Caution
​Hi Douglas, 
 
I'm sorry for the misunderstanding! Thanks for the command.
 
I attached the mas.log. 
 
Cheers,
Maxime 



​

 







De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Greve, Douglas N.,Ph.D. 
Envoyé : 6 septembre 2019 10:30
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error


 




That is the recon-all.log file. What I want is the terminal output from make_average_subject
You can capture it with 
make_average_subject [your arguments] |& tee mas.log





On 9/4/2019 9:16 PM, Maxime Perron wrote:


    External Email - Use Caution    
 
Good evening Greve,
 
Thanks for your quick answer.
 
I attached the file containing the output.
 
Best,
Maxime 




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On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D.  wrote: 


Can you send the full text of the terminal output?
 
On 9/4/19 10:44 AM, Maxime Perron wrote:

    External Email - Use Caution
 
Hi Greve,
 
The exact script is the following :

 
setenv SUBJECTS_DIR /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data
 
make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" "Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" "Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" "Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" "Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" "Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" "Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" "Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" "Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" "Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" "Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" "Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" "Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" "Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" "Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" "Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72
 
cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
mkdir ori
 
cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72
 
_
 
BrainaverageN72 is the output name.
 
Thanks,
Maxime Perron

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Greve, Douglas N.,Ph.D. 
Envoyé : 4 septembre 2019 10:37
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error
 
Is BrainaverageN72 in the subjects list?
 
On 9/3/19 12:39 PM, Maxime Perron wrote:

    External Email - Use Caution
 
​Dear Freesurfer Experts,
 
 
I have the following issue when running the make_average_subject command (
 
make_average_subject --subjects (Subjid) --out BrainaverageN72) :
 
 
Building hash of lh white
 
Building hash of lh pial
 
Building hash of rh white
 
Building hash of rh pial
 
Loading aseg from
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.000

Re: [Freesurfer] Fw: glm error

[Amrita Bedi]

External Email - Use Caution

Mean correlation values to the seed from activations of a pcc.mgh map from
each individual subject.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> mean over what? a parcellation? an activation cluster?
>
> On 10/31/2019 3:15 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
> Thank you Dr Greve, that issue is resolved.
>
> I do have another question. I’m now trying to extract mean correlation
> values to the seed from each individual subject and not sure how to go
> about this.
>
> On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz  file correctly
>> Try
>> mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i
>> */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz
>>
>> Where you have "bilat*", that should only be one folder
>>
>>
>> On 10/31/19 12:04 PM, Amrita Bedi wrote:
>> >
>> > External Email - Use Caution
>> >
>> >
>> >
>> > -- Forwarded message --
>> > From: *abedi...@citymail.cuny.edu *
>> > mailto:abedi...@citymail.cuny.edu>>
>> > Date: Thursday, October 31, 2019
>> > Subject: Fw: glm error
>> > To: Amrita Bedi mailto:amibedi...@gmail.com>>
>> >
>> >
>> >
>> >
>> > Amrita Bedi
>> > /Biomedical Engineering - Class of 2018/
>> > /The City College of New York - CUNY/
>> >
>> > 
>> 
>> > *From:* abedi...@citymail.cuny.edu 
>> > *Sent:* Thursday, October 31, 2019 12:02 PM
>> > *To:* Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > mailto:Freesurfer@nmr.mgh.harvard.edu
>> >>
>> > *Subject:* glm error
>> > Hello Freesurfer developers,
>> >
>> > I ran a seed based resting stage functional analysis for 287 subjects
>> > using the isthmus of the cingulate as a seed and now have pcc.nii.gz
>> > files in each individual subject folder. I concatenated these pcc
>> > files and am trying to run an osgm but get the following error:
>> > ERROR: DOF = 0
>> > The commands i ran for concatenating and glm are:
>> > for l in `cat sessidBOLD2`; do mri_concat --o
>> > 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz;
>> done
>> >
>> >  mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh
>> > --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi
>> > /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir
>> > all_subjects_lh_ic_pcc.TR3.glmdir
>> >
>> > The mriglmfit.log gave me the following:
>> >
>> >
>> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> > cwd
>> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to
>> 547_TR3/FSFAST
>> > cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf
>> > fsaverage lh --cortex --label
>> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to
>> 547_TR3/fsaverage/label/lh.cortex.label
>> > --glmdir all_subjects_lh_ic_pcc.TR3.glmdir
>> > sysname  Linux
>> > hostname imaging5.vaboston.lan
>> > machine  x86_64
>> > user root
>> > FixVertexAreaFlag = 1
>> > UseMaskWithSmoothing 1
>> > OneSampleGroupMean 1
>> > y
>> >  /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t
>> o547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz
>> > logyflag 0
>> > usedti  0
>> > labelmask
>> >  /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t
>> o547_TR3/fsaverage/label/lh.cortex.label
>> > maskinv 0
>> > glmdir all_subjects_lh_ic_pcc.TR3.glmdir
>> > IllCondOK 0
>> > ReScaleX 1
>> > DoFFx 0
>> >
>> > Thank you for your help.
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>
>
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>
>
>
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