[Freesurfer] Time required to run permutations

2020-11-20 Thread Basavaraju, Rakshathi 
External Email - Use Caution

Dear FS team,

Does anyone have any idea how long does the permutation computation to handle 
multiple comparisons take on a surface based analysis? The command is given 
below:

mri_glmfit-sim --glmdir rh.project.glmdir --perm 1000 3 abs --cwp  0.05 
--2spaces --bg 1

Its seems like going on forever, saying
Poll2 Job1..
Poll3 Job1.

I guessed it might stop at 1000 but its going on and on.

Any help on this would be greatly appreciated.

Thanks,
Rakshathi
Post-doc, Columbia.
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Re: [Freesurfer] mri_glmfit_sim error (Douglas N. Greve)

2020-11-05 Thread Basavaraju, Rakshathi 
ery much in advance.

Kind regards,

Agurne



Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)
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Message: 10
Date: Thu, 5 Nov 2020 11:57:20 +0100
From: Agurne Sampedro Calvete 
Subject: Re: [Freesurfer] .mgh file unknown, GLM paired analysis
{Disarmed}
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Dear FS experts,

I have removed the backslashes "\" and now it works, so problem solved.

Thank you very much.

Regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El lun., 2 nov. 2020 a las 18:27, Agurne Sampedro Calvete (<
a.sampe...@deusto.es>) escribi?:

> Dear Freesurfer Experts,
>
> I am trying to perform a paired analysis in FreeSurfer following this
> tutorial 
> https://secure-web.cisco.com/1NNzdH2MfyBVhO_al0KZMOfbMxMQvFOuKmeE95mrXN_duBKJuOP8tc0Pxq8fKqeMtcFqdYFH6fpy_cWwIVzRa-eqjc-VrDyrRyOY-inoqPPUXZqW_Pp6ILfdxZp-q8NC2kq1xFQaswZdMUwDYcWY3BCXD9zdwwCAeRUDV-lA-_xbmOWFoPavz601b977uWiM_DC0MaIZ5ld5zDWwY_JXZ4g/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1GGOE7lAk9DEhVom372ksbhQpoUEm3yIVLX4YqDE8HfMpeOEgVTUnDNdXv-5FpENZI-5FZj8E1pQJo1vbndz8QuwfXZeLFZrg8uFaXPMF0SqFXPUHmLNodW7Jl-2DSXS-2DePsn2uN1wrgmWAb4tMFpdB1JokGuLZFVIqK-5FlmBvM7eufXwSmiMuSvGQ2NREwZt2mxapAyIqfuj9JwrJS-2DMUE9Nm4DNw_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FPairedAnalysis%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D_kDbQLjFGDb_IfSuKGeqRh-mRHk_Rbl6WSEpmPyxuAo%26e%3D
>   and I
> have some problems when running the spatially smooth.
>
> I ran the following command:  mri_surf2surf --s fsaverage --hemi lh --fwhm
> 5\ --sval lh.paired-diff.thickness.mgh \ --tval
> lh.paired-diff.thickness.sm05.mgh
>
> And I found this error:
> ERROR: lh.paired-diff.thickness.mgh unknown freesurfer
>
> This file is in my subject directory, but when I see the file properties,
> in the "file type" box it says: unknown. I have read that other users have
> experienced the same error.
>
> What can I do to solve this problem?
>
> Thanks in advance.
>
> Kind regards,
>
> Agurne Sampedro
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
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Message: 11
Date: Thu, 5 Nov 2020 09:34:03 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] mri_glmfit_sim error
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"


Information about multiple comparisons correction has been pre-computed 
for various parameters, including th

[Freesurfer] mri_glmfit_sim error

2020-11-02 Thread Basavaraju, Rakshathi 
External Email - Use Caution

Hi all,

I ran a multiple comparison correction for a surface based analysis with this 
command:

mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh .05 
--2spaces

But I am getting the following error:
cannot find 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd

What might this error mean? I searched in the mail archives but could not get 
any proper answer. Kindly help me.

Thanks
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Re: [Freesurfer] Please help me. I am such with this for too long!

2020-10-28 Thread Basavaraju, Rakshathi 
ns I think control points will help to pick up
> some WM to help fuill
>
> 2.In the left hemisphere medial prefrontal (gyrus rectus) regions, the
> WM is overestimated. I presume removing WM voxels from the wm.mgz is
> the best approach?
>
> 3.The left temporal pole region is missing GM/cortex and there really
> isn?t any WM that would help with controls points or adding WM voxels.
> How can I add GM to this area?
>
> 
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
> 
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
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Message: 3
Date: Tue, 27 Oct 2020 18:11:14 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Please help me. Stuck with this for too
long!!!
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"



On 10/26/2020 3:58 PM, Basavaraju, Rakshathi wrote:
>
> External Email - Use Caution
>
> Dear Frees

[Freesurfer] Please help me. Stuck with this for too long!!!

2020-10-26 Thread Basavaraju, Rakshathi 
External Email - Use Caution

Dear Freesurfer team,

I have been trying to extract local gyrification index in a dataset according 
to a label which I have created.

1) First of all, I extracted lGI as per DKT areas, which one is lGI value in 
the ?h.pial_lgi.stats file (derived on running a lGI recon?)

# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv 
GausCurv FoldInd CurvInd
caudalanteriorcingulate  1094774   2285  3.234 0.889 
0.129 0.031   15 1.3

Is the lGI of caudal anterior cingulate 3.234 or 1.3?

2) I could register a label which I have created to the surface of individual 
subjects using mrilabel2label which ran alright, and I could view the label on 
the surface of the individual subject intact on freeview. But after that I am 
unable to extract lGI value from the designated label only using 
mris_anatomicalstats.

I used the following command: mris_anatomical_stats -l 
label/outlabelbase-0001.label -f stats/occipital_lGI.stats 
FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi

This throws the error: #MRISread: file 
'/mnt/share/projects/provenzano/Human/CHR_Rakshathi/LGI/FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE/surf/rh.pial_lgi'
 has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

Then I converted rh_pial.lgi to rh_pial.lgi.asc: mris_convert -c rh.pial_lgi 
rh.white rh.pial_lgi.asc
and then ran: mris_anatomical_stats -l label/outlabelbase-0001.label -f 
stats/occipital_lGI.stats FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi.asc

then the error: Segmentation fault (core dumped)

Kindly help me, this analysis is way overdue, and it is seeming like an endless 
tunnel only of new errors





Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute for Research on Alzheimer's Disease and the Aging Brain
Columbia University Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu
https://indiaalliance.org/fellow/rakshathi-basavaraju

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Re: [Freesurfer] [EXTERNAL] Freesurfer Digest, Vol 200, Issue 36

2020-10-23 Thread Basavaraju, Rakshathi 
blem when
>> mapping label to the single subjects.
>>
>> There is statistic difference in the area and volume
>> between?the mild traumatic brain injury patients and the
>> health control, I defined the?statistic difference region as
>> a label on the fsaverage and mapped this label to subjects by
>> the Qdec. Although the label defined on the fsaverage was
>> mapped onto all subjects successfully,the label in the
>> subjects did not match well with the inflated cortex of the
>> subjects. At the same time, the volume and area value of the
>> label have been extracted in every subject and I found that
>> there is no statistic difference between the mild traumatic
>> brain injury patients and health control. I have checked the
>> segmentation of every subjects and it was a good job done by
>> FreeSurFer. Attached figures illustrated the label mapping
>> results.
>>
>> Figure 1: the label defined on the fsaverage
>> Figure 2: the lateral view of the label in the subjects
>> Figure 3: the inferior view of the label in the subjects
>>
>> FreeSurfer
>> version:?freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>> Platform: macOS High Sierra
>>
>> I am sending this email for help since I am not sure how to
>> fix this problem. Looking forward to hearing your reply!
>> Thank you very much!
>>
>> Best wishes
>> Mengjun Li
>> Second Xiangya Hospital
>> Central South University.
>>
>>
>>
>>
>>
>> > 3.png>___
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Message: 2
Date: Mon, 19 Oct 2020 12:26:48 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Creating ROI from sig.mgh
To: 
Message-ID: <7984cce6-3e33-7681-64bf-07336a3a0...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Try using the correction for multiple comparisons (mri_glmfit-sim). Set
the CWP threshold to 1.0 to get all the clusters. It will create a table
with GI values for each cluster. Run mri_glmfit-sim with --help and/or
look on line to get more info


On 10/14/2020 3:55 PM, Basavaraju, Rakshathi wrote:
>
> External Email - Use Caution
>
> I have run a vertex based gyrification index analysis. Now I want to
> create a mask/ROI from the cluster of vertices which are above the
> threshold of 3 in sig.mgh file (p<0.001). Which command should I use
> for this purpose? Is it mri_mask? or mri_vol2roi?
>
> Next how do I extract the GI value (a numeric) from the above obtained
> ROI from individual scans?
>
> If anyone has done anything similar with thickness or volume (which I
> am sure many would have done), it would be helpful if you guided me.
> Eagerly waiting for your response.
>
> Thanks,
> Dr. Rakshathi Basavaraju (MD Psychiatry)
> Postdoctoral Research Scientist
> Taub Institute for Research on Alzheimer's Disease and the Aging Brain
> Columbia University Medical Centre
> 622 West, 168th Street, New York - 10032
> E-Mail: rb3...@cumc.columbia.edu <mailto:rb3...@cumc.columbia.edu>
> _https://urldefense.proofpoint.com/v2/url?u=https-3A__indiaalliance.org

[Freesurfer] Creating ROI from sig.mgh

2020-10-14 Thread Basavaraju, Rakshathi 
External Email - Use Caution

I have run a vertex based gyrification index analysis. Now I want to create a 
mask/ROI from the cluster of vertices which are above the threshold of 3 in 
sig.mgh file (p<0.001). Which command should I use for this purpose? Is it 
mri_mask? or mri_vol2roi?

Next how do I extract the GI value (a numeric) from the above obtained ROI from 
individual scans?

If anyone has done anything similar with thickness or volume (which I am sure 
many would have done), it would be helpful if you guided me. Eagerly waiting 
for your response.

Thanks,
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute for Research on Alzheimer's Disease and the Aging Brain
Columbia University Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu
https://indiaalliance.org/fellow/rakshathi-basavaraju

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[Freesurfer] How to account for gender in a contrast matrix

2019-06-28 Thread Basavaraju, Rakshathi 
External Email - Use Caution

Dear all FS users,
I wanted to know the way of accounting for gender in a simple regression 
analysis of cortical thickness against 2 continuous variables. Th example of 
contrast matrix given in the downloaded tutorial data for cortical thickness 
with age without accounting for gender is, 0 0 0.5 0.5 . However if we want to 
factor in gender how do we do it? Is it 0.5 0.5 0.5 0.5? or something else? 
Answers regarding same will be very much appreciated.
Thanks,
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute
Columbia University Irving Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu
http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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[Freesurfer] Unanswered question regarding including covariates in the fsgd file and the contrast matrix

2019-06-24 Thread Basavaraju, Rakshathi 
External Email - Use Caution

Hi all FS users,
I have the basic doubt of including age and gender as co-variates for a 
cortical thickness comparison between 2 groups. I read extensively many mails 
answering these questions but still could not get a satisfactory answer for the 
question.
As I have 2 discrete variables i.e. Group with 2 levels and gender with 2 
levels and one continuous variable of age my contrast matrix should be like 
this:
[0 0 0 0 0 0 0 0] which is [malegroup1 femalegroup1 malegroup2 femalegroup2 
age.malegroup1 age.femalegroup1 age.malegroup2 age.femalegroup2]
I understood that if I have to test the effect of only the groups my contrast 
matrix should be:
[0.5 0.5 -0.5 -0.5 0 0 0 0]
What should be my contrast matrix if I have to include age and gender as 
covariates respectively? I know gender cannot be included as columns of 1s and 
0s by my reading of previous mails.
In one of the mail I read that if we want to test for interaction of group and 
gender (disregarding effect of age) the contrast matrix file should be:
[0.5 -0.5 -0.5 0.5 0 0 0 0]
But is testing for gender as a covariate same as testing group*gender 
interaction? I do not feel so. Hence requesting you all to throw some clarity 
on this. If this is not the way to study gender as a covariate how else should 
the contrast matrix be written?
And regarding age should it be four 0.5s for the last 4 columns of the matrix 
if we want to study age as a covariate? Kindly let know.
Finally I want a contrast matrix that studies the group differences in cortical 
thickness covarying for the effect of age and gender. Kindly help me.

Thanks,
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute
Columbia University Irving Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu
http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288


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[Freesurfer] FW: Query regarding way to quote covariates in fsgd file

2019-06-06 Thread Basavaraju, Rakshathi 
External Email - Use Caution

Hi all FS users,
I have the basic doubt of including age and gender as co-variates for a 
cortical thickness comparison between 2 groups. I read extensively many mails 
answering these questions but still could not get a satisfactory answer for the 
question.
As I have 2 discrete variables i.e. Group with 2 levels and gender with 2 
levels and one continuous variable of age my contrast matrix should be like 
this:
[0 0 0 0 0 0 0 0] which is [malegroup1 femalegroup1 malegroup2 femalegroup2 
age.malegroup1 age.femalegroup1 age.malegroup2 age.femalegroup2]
I understood that if I have to test the effect of only the groups my contrast 
matrix should be:
[0.5 0.5 -0.5 -0.5 0 0 0 0]
What should be my contrast matrix if I have to include age and gender as 
covariates respectively? I know gender cannot be included as columns of 1s and 
0s by my reading of previous mails.
In one of the mail I read that if we want to test for interaction of group and 
gender (disregarding effect of age) the contrast matrix file should be:
[0.5 -0.5 -0.5 0.5 0 0 0 0]
But is testing for gender as a covariate same as testing group*gender 
interaction? I do not feel so. Hence requesting you all to throw some clarity 
on this. If this is not the way to study gender as a covariate how else should 
the contrast matrix be written?
And regarding age should it be four 0.5s for the last 4 columns of the matrix 
if we want to study age as a covariate? Kindly let know.
Finally I want a contrast matrix that studies the group differences in cortical 
thickness covarying for the effect of age and gender. Kindly help me.

Thanks,
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute
Columbia University Irving Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu
http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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