Re: [Freesurfer] Pial and White surface maps are not found

[Varun Chandran]

External Email - Use Caution

p.s. I am wondering whether this specific issue arises while working with
freesurfer using Linux based Virtual Machine?

On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran 
wrote:

> Hi  Yujing
>
> Thank you very much for your quick reply. Yes, I used a directory path to
> set an environment variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer)
> before running the 'recon-all' command line. However, it was not very
> helpful to obtain the pial and white surface maps and exited with some
> errors as shown in the recon-all.log (please see the file attached). Now,
> I'll try running the same command by entering the full path name of the
> directory as you suggested.
>
>
>thanks again,
>
> best,
> Varun
>
>
> On Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Varun,
>>
>>
>>
>> I’m not sure what issue that you have been running into. Can you send
>> your recon-all.log?
>>
>>
>>
>> In general, you need to
>>
>> 1. set environment variable SUBJECTS_DIR to some directory that you have
>> write permission
>>
>> 2. pass full path to T1 image to -i 
>>
>>
>>
>> Best,
>>
>>
>>
>> Yujing
>>
>>
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Varun Chandran
>> *Sent:* Wednesday, June 21, 2023 10:32 AM
>> *To:* Freesurfer support list 
>> *Subject:* [Freesurfer] Pial and White surface maps are not found
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi FS experts,
>>
>>
>>
>> It's been a few years, I used FS tools for cortical surface
>> reconstruction. Now, when I used the freesurfer 7.2 version to perform
>> cortical surface reconstruction on the T1-weighted structural MRI data, I
>> was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can
>> anyone please shed some light on this issue?
>>
>>
>>
>> command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache
>>
>>
>>
>>
>>
>> thanks,
>>
>>
>>
>> best,
>>
>> Varun
>>
>>
>>
>> --
>>
>> Varun Arunachalam Chandran, PhD
>>
>> Postdoctoral Research Associate,
>>
>> Faculty of biology, medicine and health,
>>
>> School of health sciences,
>>
>> University of Manchester,
>>
>> United Kingdom.
>>
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[Freesurfer] Pial and White surface maps are not found

[Varun Chandran]

External Email - Use Caution

Hi FS experts,

It's been a few years, I used FS tools for cortical surface reconstruction.
Now, when I used the freesurfer 7.2 version to perform cortical surface
reconstruction on the T1-weighted structural MRI data, I was unable to
obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please
shed some light on this issue?

command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache


thanks,

best,
Varun

-- 

Varun Arunachalam Chandran, PhD

Postdoctoral Research Associate,

Faculty of biology, medicine and health,

School of health sciences,

University of Manchester,

United Kingdom.

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Re: [Freesurfer] mri_glmfit and mri_glmfit-sim

[Varun Chandran]

External Email - Use Caution

Dear FS experts,

I am trying to run the cluster-wise correction by using permutation based
multiple comparison. For this, as you would know, we use: mri_glmfit-sim

In attempt to this, I tried running different options

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_AT6.fsgd doss --C
Contrast91.txt --surf fsaverage lh --cortex --glmdir glmdirlh_lat3.glmdir

mri_glmfit-sim --glmdir glmdir${i}_lat3.glmdir --cache 1.3 pos --cwp 0.05
--3spaces

Since, there was recommendations in this forum to use --perm for 1.3, I did
so

mri_glmfit --y lh.thickness.AT.10B.mgh --X design_91subjs.txt --C
Contrast_CT91.txt --surf fsaverage lh --cortex --glmdir
glmdirlh_design.glmdir

mri_glmfit-sim --glmdir glmdir_design.glmdir --perm 1000 1.3 pos --cwp 0.05
--3spaces

However, it is displayed an error message 'design matrix is not
orthogonal', though I used CT91_AT.fsgd and not the design matrix --X
option.

Despite that, I tried again starting from design matrix with the
mri_glmfit, it was ok. For the same I used, --perm for the mri-glmfit-sim.
But, it was a same orthogonalisation error message.

I am also attaching my Group Desscriptor file: .fsgd, design matrix:
GLM_all_Scan_Mim_91subjs.txt and the contrast.txt files for your reference.

It would be great, if anyone could please help sort out this issue. Thanks !

kind regards,
Varun



On Fri, Mar 13, 2020 at 10:40 PM Douglas N. Greve 
wrote:

> It looks like you are using gender as a continuous variable. You should
> set up two classes, one for male one for female. You can then test for the
> AT slope with a contrast of
> 0 0 0 0 0.5 0.5
> you don't need separate pos and neg contrasts
>
> For mri_glmfit-sim, a threshold of 1.3 (p<.05) is way too liberal for the
> MCZ simulation. I would use permutation. See
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 3/12/2020 6:30 AM, Varun Chandran wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> I am looking at the relationship between the cortical thickness and a
> behaviour measure, while controlling for the effects of age and gender. In
> this analysis, I am using CT_AT.fsgd, contrast_pos.txt and a
> contrast_neg.txt.
>
> GroupDescriptorFile 1
> Title Autistictraits
> Class AT
> Variables Age Gender   AT
>
> Input   Con_P001   AT   -4.142-0.42821
> Input   Con_P002   AT   -8.142-0.42831
>
> My separate two contrast files:
>
> Contrast_pos.txt  0  0   0 1
>
> Contrast_neg.txt  0  0   0 -1
>
> mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
> Contrast91_pos.txt --surf fsaverage lh --cortex --glmdir
> glmdirlhposlat.glmdir
>
> mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
> Contrast91_neg.txt --surf fsaverage lh --cortex --glmdir
> glmdirlhneglat.glmdir
>
> mri_glmfit-sim --glmdir glmdirlhposlat.glmdir --cache 1.3 pos --cwp 0.05
>
> mri_glmfit-sim --glmdir glmdirlhneglat.glmdir --cache 1.3 neg --cwp 0.05
>
> By changing the commands appropriately, I am looking at the right
> hemisphere too.
>
> Can anyone please help me to clarify, if I am applying the command lines
> correctly? Any sort of help would be very much appreciated. Thanks !
>
> best,
> Varun Arunachalam Chandran
> PhD scholar (Neurosciences)
>
> *School of Psychology and Clinical Language Sciences,  University of
> Reading, Harry Pitt Building, *
> *Whiteknights campus, Reading-RG6 7BE,*
> *Berkshire, United Kingdom.*
>
>
>
>
>
>
>
> ___
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>
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1.00e+002.10e+01-4.142000e+00   -4.28e-01   
1.00e+003.10e+01-8.142000e+00   -4.28e-01   
1.00e+002.00e+01-6.142000e+00   5.72e-01
1.00e+001.90e+01-8.142000e+00   -4.28e-01   
1.00e+001.10e+01-5.142000e+00   -4.28e-01   
1.00e+001.10e+01-3.142000e+00   -4.28e-01   
1.00e+003.00e+00-5.142000e+00   5.72e-01
1.00e+009.00e+00-6.142000e+00   -4.28e-01   
1.00e+003.30e+01-1.142000e+00   5.72e-01
1.00e+001.10e+01-1.014200e+01   -4.28e-01   
1.00e+007.00e+00-5.142000e+00   -4.28e-01   
1.00e+001.70e+01-7.142000e+00   -4.28e-01   
1.00e+001.30e+01-8.142000e+00   5.72e

Re: [Freesurfer] mri_glmfit and mri_glmfit-sim

[Varun Chandran]

External Email - Use Caution

Dear Doug,

Thank you very much for clarifying my doubt :)

kind regards,
Varun

On Fri, Mar 13, 2020 at 10:40 PM Douglas N. Greve 
wrote:

> It looks like you are using gender as a continuous variable. You should
> set up two classes, one for male one for female. You can then test for the
> AT slope with a contrast of
> 0 0 0 0 0.5 0.5
> you don't need separate pos and neg contrasts
>
> For mri_glmfit-sim, a threshold of 1.3 (p<.05) is way too liberal for the
> MCZ simulation. I would use permutation. See
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 3/12/2020 6:30 AM, Varun Chandran wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> I am looking at the relationship between the cortical thickness and a
> behaviour measure, while controlling for the effects of age and gender. In
> this analysis, I am using CT_AT.fsgd, contrast_pos.txt and a
> contrast_neg.txt.
>
> GroupDescriptorFile 1
> Title Autistictraits
> Class AT
> Variables Age Gender   AT
>
> Input   Con_P001   AT   -4.142-0.42821
> Input   Con_P002   AT   -8.142-0.42831
>
> My separate two contrast files:
>
> Contrast_pos.txt  0  0   0 1
>
> Contrast_neg.txt  0  0   0 -1
>
> mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
> Contrast91_pos.txt --surf fsaverage lh --cortex --glmdir
> glmdirlhposlat.glmdir
>
> mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
> Contrast91_neg.txt --surf fsaverage lh --cortex --glmdir
> glmdirlhneglat.glmdir
>
> mri_glmfit-sim --glmdir glmdirlhposlat.glmdir --cache 1.3 pos --cwp 0.05
>
> mri_glmfit-sim --glmdir glmdirlhneglat.glmdir --cache 1.3 neg --cwp 0.05
>
> By changing the commands appropriately, I am looking at the right
> hemisphere too.
>
> Can anyone please help me to clarify, if I am applying the command lines
> correctly? Any sort of help would be very much appreciated. Thanks !
>
> best,
> Varun Arunachalam Chandran
> PhD scholar (Neurosciences)
>
> *School of Psychology and Clinical Language Sciences,  University of
> Reading, Harry Pitt Building, *
> *Whiteknights campus, Reading-RG6 7BE,*
> *Berkshire, United Kingdom.*
>
>
>
>
>
>
>
> ___
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>
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[Freesurfer] mri_glmfit and mri_glmfit-sim

[Varun Chandran]

External Email - Use Caution

Dear FS experts,

I am looking at the relationship between the cortical thickness and a
behaviour measure, while controlling for the effects of age and gender. In
this analysis, I am using CT_AT.fsgd, contrast_pos.txt and a
contrast_neg.txt.

GroupDescriptorFile 1
Title Autistictraits
Class AT
Variables Age Gender   AT

Input   Con_P001   AT   -4.142-0.42821
Input   Con_P002   AT   -8.142-0.42831

My separate two contrast files:

Contrast_pos.txt  0  0   0 1

Contrast_neg.txt  0  0   0 -1

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
Contrast91_pos.txt --surf fsaverage lh --cortex --glmdir
glmdirlhposlat.glmdir

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C
Contrast91_neg.txt --surf fsaverage lh --cortex --glmdir
glmdirlhneglat.glmdir

mri_glmfit-sim --glmdir glmdirlhposlat.glmdir --cache 1.3 pos --cwp 0.05

mri_glmfit-sim --glmdir glmdirlhneglat.glmdir --cache 1.3 neg --cwp 0.05

By changing the commands appropriately, I am looking at the right
hemisphere too.

Can anyone please help me to clarify, if I am applying the command lines
correctly? Any sort of help would be very much appreciated. Thanks !

best,
Varun Arunachalam Chandran
PhD scholar (Neurosciences)

*School of Psychology and Clinical Language Sciences, University of
Reading, Harry Pitt Building, *
*Whiteknights campus, Reading-RG6 7BE,*
*Berkshire, United Kingdom.*
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[Freesurfer] Request for access to the freesurfer mailing list

[Varun Chandran]

External Email - Use Caution

Dear Freesurfer committee,

I would like to use the freesurfer mailing list to post my doubts about the
cortical thickness analysis pipeline. Therefore, could you please provide
me the access to post my doubts on the same?


  thanks,

kind regards,
Varun Arunachalam Chandran
PhD in Neurosciences,
School of Psychology and Language Sciences,
University of Reading,
Berkshire, UK
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