date:20190808

Re: [Freesurfer] Hippocampal subfields

2019-08-08 Thread Iglesias Gonzalez, Juan E.

Dear Zheng,
I believe you ran out of memory. How much RAM does your machine have? You need 
about 10GB to run this.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Friday, 9 August 2019 at 01:19
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Dear /Eugenio,

Here is the log files and all results for one subject as the attachments. I 
have run a lots of subjects and all result directories didn't include 
l(r)h.hippoSfLabels-T1.v10.mgz file.

Sincerely,
Zheng



At 2019-08-08 09:49:30, "Iglesias Gonzalez, Juan E." 
 wrote:

Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 21:19
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields


External Email - Use Caution
Hi exports,

I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.

Sincerely,
Zheng






从网易163邮箱发来的云附件
[Image removed by 
sender.]
hippocampal-subfields-T1.log
 (112.5K, 2019年8月24日 13:06 到期)
下载
[Image removed by 
sender.]
CQMS004.zip
 (359.89M, 2019年8月24日 12:57 到期)
下载





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Re: [Freesurfer] Hippocampal subfields

2019-08-08 Thread 郑凤莲

External Email - Use Caution

Dear /Eugenio,


Here is the log files and all results for one subject as the attachments. I 
have run a lots of subjects and all result directories didn't include 
l(r)h.hippoSfLabels-T1.v10.mgz file.


Sincerely,
Zheng





At 2019-08-08 09:49:30, "Iglesias Gonzalez, Juan E." 
 wrote:


Dear Zheng,

Can you please send us the log files?

Kind regards,

/Eugenio

 

-- 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

 

 

From:  on behalf of 郑凤莲 

Reply-To: Freesurfer support list 
Date: Wednesday, 7 August 2019 at 21:19
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields

 

External Email - Use Caution

Hi exports,

 

I am using FS6.0 to segment hippocampus. I run "recon-all -s bert 
-hippocampal-subfields-T1" and it said "recon all bert finished without error". 
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And 
in tmp directory, there are two directories, "hippoSF_T1_v10_left" and 
"hippoSF_T1_v10_right". But in these two directories, the 
l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I 
need your help. Thanks very muxh in advance.

 

Sincerely,

Zheng






 

从网易163邮箱发来的云附件
hippocampal-subfields-T1.log (112.5K, 2019年8月24日 13:06 到期)
下载
CQMS004.zip (359.89M, 2019年8月24日 12:57 到期)
下载___
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[Freesurfer] Avoiding or removing overlap when converting surface labels to volume

2019-08-08 Thread Jacob Miller

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Hi Freesurfer team,

I am transforming several adjacent surface labels into volume ROIs, using
*mri_label2vol*. When doing so, there seems to be some possibly unavoidable
overlap in a small number of voxels in the volume ROIs. Is there any way to
avoid these labels from overlapping when transformed into the volume? I see
that *mri_label2vol* takes an --annot flag, would this help in avoiding
overlap in the outputs?

Otherwise, I can remove the overlapping voxels int he nifti file outputs,
but I was wondering if the algorithm had any options to do this as part of
the surface-to-volume transform.

Thanks so much!
Jacob

-- 

Jacob Miller
Graduate Student, D'Esposito Lab
Helen Wills Neuroscience Institute (HWNI)
University of California, Berkeley

https://despolab.berkeley.edu/
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Re: [Freesurfer] TRACULA - runlist longer than subject list

2019-08-08 Thread Yendiki, Anastasia

Hi Daniel - Can you please attach the dmrirc and trac-all.log files in their 
entirety? Thanks!


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Thursday, August 8, 2019 9:07:31 AM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA - runlist longer than subject list


External Email - Use Caution

Hello,

When trying to run TRACULA on my data I keep getting the following error.

domainname: Command not found.

INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy

INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac

Actual FREESURFER_HOME /Applications/freesurfer

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: current FREESURFER_HOME does not match that of previous processing.

Current: /Applications/freesurfer

Previous: /Applications/freesurfer_dev

/Volumes/DANIEL/trac-all -c 
/Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log 
/Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd 
/Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd

domainname: Command not found.

ERROR: run list is longer than subject list


I have never had this issue before and have tried multiple options for the run 
list from () to (1 2 3) to include a number for every subject. However, I 
always get this error.


I wonder if there is some issue with the formatting this go around that could 
be causing the issue but I can't find it.


Below is what I have for the initial part of my dmrirc folder.


# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/


# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /Volumes/DANIEL/dti_Tracy/trac


# Subject IDs (one per time point per subject)

#

set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018 HMN020 
HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050 HMN055 HMN057 
HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085 HMN087 HMN088 HMN095 
HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105 HMN108 HMN110 HMN112 HMN113 
HMN115 HMN118 HMN120 HMN121 HMN123 HMN135 HMN141 HMN144 HMN152 HMN156 HMN160 
HMN163 HMN175 HMN180 HMN186 HMN187 HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 
HMN200 HMN201)


# Longitudinal base template subject IDs (one for each time point above)

#

set baselist = ()


# In case you want to analyze only Huey and Louie

# Default: Run analysis on all time points and subjects

#1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 
56 57 58 59 60 61 62 63 64 65 66


set runlist = ()


# Input diffusion DICOMs (file names relative to dcmroot)

# If original DICOMs don't exist, these can be in other image format

# but then the gradient table and b-value table must be specified (see below)

#

set dcmroot = /Volumes/DANIEL/Tracy/HMN_W1

set dcmlist = ( HMN002/image01.dcm HMN003/image01.dcm 
HMN005/image01.dcm HMN006/image01.dcm HMN007/image01.dcm 
HMN011/image01.dcm HMN014/image01.dcm HMN018/image01.dcm 
HMN020/image01.dcm HMN021/image01.dcm HMN022/image01.dcm 
HMN025/image01.dcm HMN029/image01.dcm HMN035/image01.dcm 
HMN037/image01.dcm HMN039/image01.dcm HMN045/image01.dcm 
HMN050/image01.dcm HMN055/image01.dcm HMN057/image01.dcm 
HMN060/image01.dcm HMN064/image01.dcm HMN065/image01.dcm 
HMN069/image01.dcm HMN072/image01.dcm HMN073/image01.dcm 
HMN079/image01.dcm HMN085/image01.dcm HMN087/image01.dcm 
HMN088/image01.dcm HMN095/image01.dcm HMN097/image01.dcm 
HMN098/image01.dcm HMN099/image01.dcm HMN101/image01.dcm 
HMN102/image01.dcm HMN103/image01.dcm HMN105/image01.dcm 
HMN108/image01.dcm HMN110/image01.dcm HMN112/image01.dcm 
HMN113/image01.dcm HMN115/image01.dcm HMN118/image01.dcm 
HMN120/image01.dcm HMN121/image01.dcm HMN123/image01.dcm 
HMN135/image01.dcm HMN141/image01.dcm HMN144/image01.dcm 
HMN152/image01.dcm HMN156/image01.dcm HMN160/image01.dcm 
HMN163/image01.dcm HMN175/image01.dcm HMN180/image01.dcm 
HMN186/image01.dcm HMN187/image01.dcm HMN189/image01.dcm 
HMN190/image01.dcm HMN191/image01.dcm HMN193/image01.dcm 
HMN195/image01.dcm HMN196/image01.dcm HMN200/image01.dcm 
HMN201/image01.dc)


Any help debugging the issue would be greatly appreciated!


Daniel Callow

PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
___

Re: [Freesurfer] TRACULA empty bbr maps after trac-all -prep

2019-08-08 Thread Yendiki, Anastasia

Hi Fred - What program are you using to display these? Any chance that the 
volumes are not actually all zero but that they're just not displayed correctly 
for whatever reason?


Have you tried opening these two volumes in freeview at the same time?


/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz


/media/freds/LinuxData2/FIS_ESTHERCUBO_RESO/Tractografia_FIS_CUBO/TractHipoResult//T1_GONZALEZ_DE_LAS_HERAS_TERESA_NeuroNavegador_Sag_FSPGR_3D_geometry_activo_GD_177643_NeuroNavegador_Sag_FSPGR_3D_geometry_activo_GD_20190403164820_3/dmri/brain_anat_mni.nii.gz


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fred Sampedro 

Sent: Thursday, August 8, 2019 5:35:50 AM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA empty bbr maps after trac-all -prep


External Email - Use Caution

Dear TRACULA experts, dear Anastasia,

I've been successfully using TRACULA for a while with different DTI images from 
different scanners (siemens, philips...). Now I am working with GE DTI data and 
whereas the trac-all -prep command went well, and 
$subject/dmri/dtifit_FA.nii.gz and dtifit_MD.nii.gz look fine, 
$subject/dmri/mni/dtifit_FA.bbr.nii.gz and all mni-space maps are empty (see 
pictures attached). I also attach the trac-all.log file. and bvals/bvecs that 
were generated by trac-all directly from the dicom images.

What could have gone wrong?
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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

2019-08-08 Thread Iglesias Gonzalez, Juan E.

Please try using the 1mm version of the segmentation in FreeSurfer space.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Jessica Bourgin 

Reply-To: Freesurfer support list 
Date: Thursday, 8 August 2019 at 11:58
To: freesurfer 
Subject: Re: [Freesurfer] Transform hippocampal/amygdala segmentation to 
another space


External Email - Use Caution
Dear Juan Eugenio,

Thank you for these precisions.

Following the guidelines of FSL, I computed the following sequence on my 
structural image :

bet my_structural my_betted_structural
flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural 
-omat my_affine_transf.mat
fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf 
--config=T1_2_MNI152_2mm
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural 
--warp=my_nonlinear_transf --out=my_warped_structural

The warped structural image overlapped nicely with the atlas.

However, when I compute the following command on the segmentations :

applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm 
--in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf 
--out=my_warped_lh
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm 
--in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf 
--out=my_warped_rh

The segmentations do not appear on the atlas nor the structural image.

Do you know how to solve this problem ?

Thanks for your help.

PS: I used FSL for registration because I don't know how to do that with 
Freesurfer.

Jessica BOURGIN
Laboratoire de Psychologie et Neurocognition
CNRS UMR 5105
Université Savoie Mont Blanc (USMB)
BP 1104
73011 Chambery Cedex France
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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space

2019-08-08 Thread Jessica Bourgin

External Email - Use Caution

Dear Juan Eugenio, 

Thank you for these precisions. 

Following the guidelines of FSL, I computed the following sequence on my 
structural image : 

bet my_structural my_betted_structural 
flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural 
-omat my_affine_transf.mat 
fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf 
--config=T1_2_MNI152_2mm 
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural 
--warp=my_nonlinear_transf --out=my_warped_structural 

The warped structural image overlapped nicely with the atlas. 

However, when I compute the following command on the segmentations : 

applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm 
--in=freesurfer/lh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf 
--out=my_warped_lh 
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm 
--in=freesurfer/rh.hippoAmygLabels-T1.v21.nii.gz --warp=my_nonlinear_transf 
--out=my_warped_rh 

The segmentations do not appear on the atlas nor the structural image. 

Do you know how to solve this problem ? 

Thanks for your help. 

PS: I used FSL for registration because I don't know how to do that with 
Freesurfer. 

Jessica BOURGIN 
Laboratoire de Psychologie et Neurocognition 
CNRS UMR 5105 
Université Savoie Mont Blanc (USMB) 
BP 1104 
73011 Chambery Cedex France 
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Re: [Freesurfer] SegmentHA_T1.sh hippocampal sub-field issue

2019-08-08 Thread Iglesias Gonzalez, Juan E.

Ouch. Is the aseg also like that?
Cheers,
/E

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Thursday, 8 August 2019 at 08:20
To: Freesurfer support list 
Subject: [Freesurfer] SegmentHA_T1.sh hippocampal sub-field issue


External Email - Use Caution
Hello,

When using segmentHA_T1.sh on one of my subjects the left hippocampus ROI seems 
to spill over a lot into white matter and other gray matter regions. See 
attached picture. Is there a way to fix this or improve the hippocampal 
segmentation? Or will I have to scrap this subject's data? I have also included 
the scan log.

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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[Freesurfer] TRACULA - runlist longer than subject list

2019-08-08 Thread Daniel Callow

External Email - Use Caution

Hello,

When trying to run TRACULA on my data I keep getting the following error.

domainname: Command not found.

INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy

INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac

Actual FREESURFER_HOME /Applications/freesurfer

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: current FREESURFER_HOME does not match that of previous processing.

Current: /Applications/freesurfer

Previous: /Applications/freesurfer_dev

/Volumes/DANIEL/trac-all -c
/Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log
/Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd
/Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd

domainname: Command not found.

ERROR: run list is longer than subject list


I have never had this issue before and have tried multiple options for the
run list from () to (1 2 3) to include a number for every subject. However,
I always get this error.


I wonder if there is some issue with the formatting this go around that
could be causing the issue but I can't find it.


Below is what I have for the initial part of my dmrirc folder.


*# FreeSurfer SUBJECTS_DIR*

*# T1 images and FreeSurfer segmentations are expected to be found here*

*# *

setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/


*# Output directory where trac-all results will be saved*

*# Default: Same as SUBJECTS_DIR*

*#*

set dtroot = /Volumes/DANIEL/dti_Tracy/trac


*# Subject IDs (one per time point per subject)*

*#*

set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018
HMN020 HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050
HMN055 HMN057 HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085
HMN087 HMN088 HMN095 HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105
HMN108 HMN110 HMN112 HMN113 HMN115 HMN118 HMN120 HMN121 HMN123 HMN135
HMN141 HMN144 HMN152 HMN156 HMN160 HMN163 HMN175 HMN180 HMN186 HMN187
HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 HMN200 HMN201)


*# Longitudinal base template subject IDs (one for each time point above)*

*#*

set baselist = ()


*# In case you want to analyze only Huey and Louie*

*# Default: Run analysis on all time points and subjects*

*#1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52
53 54 55 56 57 58 59 60 61 62 63 64 65 66*


set runlist = ()


*# Input diffusion DICOMs (file names relative to dcmroot)*

*# If original DICOMs don't exist, these can be in other image format*

*# but then the gradient table and b-value table must be specified (see
below)*

*#*

set dcmroot = /Volumes/DANIEL/Tracy/HMN_W1

set dcmlist = ( HMN002/image01.dcm HMN003/image01.dcm
HMN005/image01.dcm HMN006/image01.dcm HMN007/image01.dcm
HMN011/image01.dcm HMN014/image01.dcm HMN018/image01.dcm
HMN020/image01.dcm HMN021/image01.dcm HMN022/image01.dcm
HMN025/image01.dcm HMN029/image01.dcm HMN035/image01.dcm
HMN037/image01.dcm HMN039/image01.dcm HMN045/image01.dcm
HMN050/image01.dcm HMN055/image01.dcm HMN057/image01.dcm
HMN060/image01.dcm HMN064/image01.dcm HMN065/image01.dcm
HMN069/image01.dcm HMN072/image01.dcm HMN073/image01.dcm
HMN079/image01.dcm HMN085/image01.dcm HMN087/image01.dcm
HMN088/image01.dcm HMN095/image01.dcm HMN097/image01.dcm
HMN098/image01.dcm HMN099/image01.dcm HMN101/image01.dcm
HMN102/image01.dcm HMN103/image01.dcm HMN105/image01.dcm
HMN108/image01.dcm HMN110/image01.dcm HMN112/image01.dcm
HMN113/image01.dcm HMN115/image01.dcm HMN118/image01.dcm
HMN120/image01.dcm HMN121/image01.dcm HMN123/image01.dcm
HMN135/image01.dcm HMN141/image01.dcm HMN144/image01.dcm
HMN152/image01.dcm HMN156/image01.dcm HMN160/image01.dcm
HMN163/image01.dcm HMN175/image01.dcm HMN180/image01.dcm
HMN186/image01.dcm HMN187/image01.dcm HMN189/image01.dcm
HMN190/image01.dcm HMN191/image01.dcm HMN193/image01.dcm
HMN195/image01.dcm HMN196/image01.dcm HMN200/image01.dcm
HMN201/image01.dc)


Any help debugging the issue would be greatly appreciated!


*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

2019-08-08 Thread Reza Rahmanzadeh

External Email - Use Caution

Dear Doug,


Please find the enclosed the output of mris_preproc and .log output of 
terminal. I viewed the output in freevew as overlay, and again it seems that 
values getting 0 after mris_preproc.



Thanks,

Reza


From: Greve, Douglas N.,Ph.D. 
Sent: Wednesday, August 7, 2019 6:03:58 PM
To: Reza Rahmanzadeh
Cc: Freesurfer support list
Subject: Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for 
help

Run mris_preproc with a single subject and send the terminal output

On 8/7/19 11:47 AM, Reza Rahmanzadeh wrote:
>  External Email - Use Caution
>
> Yes, i checked -projfrac 0.5 with old or new mris_preproc but didn’t work. I 
> checked all registration, they are perfect.
>
>> On 7 Aug 2019, at 17:29, Greve, Douglas N.,Ph.D.  
>> wrote:
>>
>> If you do not specify --projfrac-avg, does it come out as non-zero? If
>> so, I would think that it is a problem with the registration. Have you
>> checked the registrations?
>>
>>> On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
>>>  External Email - Use Caution
>>>
>>> It means that for any given subjects i’ve had one -iv argument and then for 
>>> mri_glmfit i used .fsgd file with the same order.
>>>
 On 7 Aug 2019, at 17:23, Reza Rahmanzadeh  
 wrote:

 External Email - Use Caution

 Yes, for mris_preproc:

 mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
 lh.NDI_inflated.avg.mgh --iv  
 

> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh  
> wrote:
>
> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out 
> lh.NDI_inflated.avg.mgh
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