Re: [Freesurfer] Mean diffusivity on cortex?

[Yendiki, Anastasia]

You can use the wmparc, which includes ROIs of the WM underlying each cortical 
area, right below the grey-white boundary surface. These are the relevant 
tutorials:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield 
[shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 2:03 AM
To: Freesurfer Support List
Subject: [Freesurfer] Mean diffusivity on cortex?

Hi DTI Experts,

Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?

DT_RECON has been completed in Freesurfer.

Thank you.

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Re: [Freesurfer] Freesurfer PIB PET image processing

[M Janani]

Thanks for your support Douglas. 

I have processed my PIB PET images using PETSURFER. It works fine.

I have one more query. Could you please help in computing the PiB mean value 
and intensity value for the ROIs.

Regards,
Janani


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 10 August 2017 20:06
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer PIB PET image processing

do you mean to run the anatomical analysis on them? No.


On 08/10/2017 05:23 AM, M Janani wrote:
> Is it correct to process the PiB images using Freesurfer ?
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: 10 August 2017 03:41
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>
> We do not have any thing to specifically analyze PiB. You can look at 
> the PETsurfer page for more general instructions
>
>
> On 08/09/2017 02:15 AM, M Janani wrote:
>> Hi Team,
>>
>> I apologize, I am new to Freesurfer.
>>
>> Currently we are processing PIB PET images.
>>
>>  When we compare the SPM data along with FREESURFER 
>> outputs. We were able to see a large variation in the values.
>>
>>  Could you please guide us in processing PIB PET 
>> images in Freesurfer?
>>
>>  Since the signal of a PET image is very weak, we 
>> used MRI image as a guide to map it to Standard brain.
>>
>>  How does Freesurfer process in this case?
>>
>>  Your help would be grateful.
>>
>> Regards,
>>
>> Janani
>>
>>
>>
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal 
cortical thickness comparisons between group? If the answer is yes, are there 
recommended on smoothing ?
DT_RECON has been completed in Freesurfer.

Thank you.
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[Freesurfer] Matlab 2016b and localGI

[Juranek, Jenifer]

Hi,

Hope someone can identify my user error...I've listed below key bits of info 
(system info, cmdline and error message, echo $PATH, cat .bashrc, cat 
startup.m).

Really appreciate someone taking a look and walking me through a solution to my 
error?

Many Thanks!

Jenifer


1) Running Freesurfer_v6 on RHEL Centos7.3

and matlab 2016b (with imaging processing toolbox)

2) recon-all -s  -localGI

returns the following:

#@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017

 mris_compute_lgi --i lh.pial

ERROR: Matlab is required to run mris_compute_lgi!
Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19 11:24:13 
EDT 2016 x86_64 x86_64 x86_64 GNU/Linux


3) matlab is in my path

[jjuranek@localhost subjects]$ echo $PATH
/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/home/jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab


4) my .bashrc file is as follows

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

# User specific aliases and functions

export FREESURFER_HOME=/home/jjuranek/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

matlab=/home/jjuranek/matlab/R2016b/bin/matlab
alias matlab=$matlab

export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab

#/home/jjuranek/matlab/R2016b/bin/matlab
#MATLAB is selecting SOFTWARE OPENGL rendering.


5) my startup.m file is as follows

% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
addpath(genpath(fsmatlab));
end
clear fshome fsmatlab;
%-%

% FreeSurfer FAST %
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-%

% FreeSurfer LGI %
FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;

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Re: [Freesurfer] Cortical thickness map for a pediatric case

[Martin Reuter]

Hi Sneha, 

I don’t know why this fails. There could be many reasons. Firstmost, the 
longitudinal stream assumes that head size is constant, which is probably not 
the case in your data. Looking at the log file however, it seems that recon-all 
stops in the NU correction step that comes before talairach registration and it 
is unclear why. 

Take a look at the orig.mgz (the template image). If that looks bad, like to 
shadow images that don’t align, then the robust_template registration code 
fails before. If it looks like a brain (maybe a little blurry, but otherwise 
OK), then It would be the NU correct. 

Anyway I don’t think you should spend to much time debugging for the reason 
above. Instead you could simply use the cross sectional stream. Then register 
all thickness files to fsaverage (mri_preproc), then do a pairwise subtract or 
Percent change computation and after that a group analysis on the thickness 
differences across time. I think mri_concat can do pairwise differences. And 
you would have to setup the GLM on your own with mri_glmfit or create a qdec 
table where you only have one entry per subject. 

Best, Martin


> On 10. Aug 2017, at 17:02, Sneha Pandya  wrote:
> 
> Hi Bruce and Martin,
> 
> Wanted to follow up and see if you'll got a chance to look at the error and 
> if I could try out something?
> 
> Thanks,
> Sneha
> From: Sneha Pandya
> Sent: Tuesday, August 8, 2017 11:29:23 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
>  
> Thank you Bruce, sure thing :) 
> 
> Regards,
> Sneha
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: Monday, August 7, 2017 6:21:57 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
>  
> thanks Sneha
> 
> you'll probably need to wait until tomorrow for Martin to read his email :)
> 
> cheers
> Bruce
> 
> On Mon, 7 Aug 2017, Sneha Pandya wrote:
> 
> > 
> > Hi Bruce,
> > 
> > 
> > Sure, please see highlighted below part of screen output showing the error.
> > Since I ran the command within a screen sesison I have saved executed screen
> > session to a log file. Find attached log file with output of entire run. 
> > Please
> > let me know if any other files are required and if attached log file could 
> > be
> > interpreted.
> > 
> > 
> > Read individual LTAs
> > Writing  LTA to file ped1_base_to_ped1_0.lta...
> > mri_concatenate_lta successful.
> > 
> >  mri_concatenate_lta -invert1 ped1_1_to_ped1_base.lta identity.nofile
> > ped1_base_to_ped1_1.lta
> > 
> > invert the first LTA before applying it
> > Read individual LTAs
> > Writing  LTA to file ped1_base_to_ped1_1.lta...  
> > mri_concatenate_lta successful.
> > 
> >  mri_concatenate_lta -invert1 ped1_2_to_ped1_base.lta identity.nofile
> > ped1_base_to_ped1_2.lta
> > 
> > invert the first LTA before applying it
> > Read individual LTAs
> > Writing  LTA to file ped1_base_to_ped1_2.lta...  
> > mri_concatenate_lta successful.
> > 
> >  mri_concatenate_lta -invert1 ped1_3_to_ped1_base.lta identity.nofile
> > ped1_base_to_ped1_3.lta
> > 
> > invert the first LTA before applying it
> > Read individual LTAs
> > Writing  LTA to file ped1_base_to_ped1_3.lta...  
> > mri_concatenate_lta successful.
> > 
> >  mri_concatenate_lta -invert1 ped1_4_to_ped1_base.lta identity.nofile
> > ped1_base_to_ped1_4.lta
> > 
> > invert the first LTA before applying it
> > Read individual LTAs
> > Writing  LTA to file ped1_base_to_ped1_4.lta...  
> > mri_concatenate_lta successful.
> > #
> > #@# MotionCor Wed Jul 26 14:04:13 EDT 2017
> > 
> >  mri_add_xform_to_header -c
> > /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/talairach.xfm
> > /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz
> > /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz
> > 
> > INFO: extension is mgz
> > #
> > #@# Talairach Wed Jul 26 14:04:14 EDT 2017
> > /shared_data2/sneha/MSKCC_Processed/ped1_base/mri
> > 
> >  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> > orig.mgz --o orig_nu.mgz
> > 
> > Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 
> > x86_64
> > x86_64 x86_64 GNU/Linux
> > 
> > recon-all -s ped1_base exited with ERRORS at Wed Jul 26 14:04:17 EDT 2017
> > 
> > For more details, see the log file
> > /shared_data2/sneha/MSKCC_Processed/ped1_base/scripts/recon-all.log
> > To report a problem, see 
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=DwIDbA&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=BoRZLsXqqVT6-Qe8baTB-uaC5VkO8MylpF2Pge0ejiI&s=80fR0T3L4F8R5icMg6uqKyEXyWyEbcpI5AFOF2UVRzo&e=
> >  
> > 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

Sure. Please make sure you have as much as spare disk space as you can. 

> On Aug 10, 2017, at 4:12 PM, Z Hessam  wrote:
> 
> it seems that I should run it again
> thank you for your helps
> best regards
> 
> On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang  > wrote:
> OK. Actually I was wrong, the file has size of 0! I don’t know what happened 
> when you installed freesurfer or ran recon-all, but the file was not properly 
> written...
> 
>> On Aug 10, 2017, at 9:34 AM, Z Hessam > > wrote:
>> 
>> I copy the *.tar.gz file, and open and install the program by terminal. I am 
>> confused because that work last week for this data, but now, this doesn't 
>> work.
>> for other datasets, i copy dicom files, then convert them with " recon-all 
>> -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 
>> fat_fh23" command to *.mgz, and then i use the "recon-all -s  -all " 
>> command in linux terminal.
>> 
>> On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang > > wrote:
>> How did you put the data on your drive?
>> 
>>> On Aug 10, 2017, at 9:25 AM, Z Hessam >> > wrote:
>>> 
>>> I didn't copy the file, and drive has 3.7GB free space
>>> 
>>> On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang >> > wrote:
>>> Wait, the file size looks too small. Only 1590 bytes. Did the data get 
>>> copied properly? Is your drive full? 
>>> 
 On Aug 10, 2017, at 4:40 AM, Z Hessam >>> > wrote:
 
 it shows:
 
 -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
 
 
 On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang >>> > wrote:
 Hmm, if you run:
 
 ls -l 
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
 
 what does it show?
 
> On Aug 9, 2017, at 4:47 PM, Z Hessam  > wrote:
> 
> of course:
> 
> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
> 
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> MRIread failed: Unable to read from 
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> MRIread failed: Unable to read from 
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> 
> thanks a lot for your attention 
> 
> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang  > wrote:
> Can you copy and paste the exact command line you ran and the error 
> message?
> 
> Ruopeng
> 
> 
> On 08/09/2017 02:21 PM, Z Hessam wrote:
>> 
>> I try it without \ chars, works for some other subjects
>> but it doesn't work for one of them,and now I can even open it with GUI, 
>> while I could open it before.
>> It seems that is time variant!
>> Should I run "recon-all ..." again for that subject?
>> 
>> 
>> 
>> 
>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl 
>> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>> can you try it without all the \ characters?  You shouldn't need them if 
>> it's all on one line
>> 
>> On Wed, 9 Aug 2017, Z Hessam wrote:
>> 
>> 
>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> MRIread failed: Unable to read from
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> 
>> 
>> I use the example 4 in the "download and install" page of site
>> 
>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl > >
>> wrote:
>> 
>>   hmmm, that looks ok, but it's hard to tell with all the
>>   backslashes and blank lines and such. Can you send the full
>>   command on a single line (e.g. by hitting up-arrow in the
>

Re: [Freesurfer] mri_surf2vol

[Douglas N Greve]

Try using mri_label2vol with the ribbon.mgz file. That has a 
segmenentation of everything inside the white surface.


On 08/10/2017 03:58 PM, Rockers, Elijah D. wrote:
> I am attempting to create a volume from a surface. My ultimate goal is 
> to obtain a mask that includes everything "inside" the white matter 
> surfaces. wm.mgz is close, but it would nicer to just get a mask from 
> lh.white and rh.white. I would like these masks to be in the subject's 
> native space. However I try the following command and see the 
> resulting error:
>
> mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi 
> lh --identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz
>
> gdiagno = -1
> Using identity matrix for registration
> mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file
> mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header
>
> I'm obviously doing something wrong here, but I'm not sure what needs 
> to change. I used --identity because native space, and it wouldn't let 
> me run the command without specifying --template, which I'm not sure I 
> understand, because, again, target is native space. Please illuminate me,
>
> Thank you,
>
> - Eli
>
> Houston Methodist. Leading Medicine.
>
> /U.S. News & World Report/ has recognized Houston Methodist as one of 
> the nation’s top 20 hospitals, placing it for the second time on the 
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

it seems that I should run it again
thank you for your helps
best regards

On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang 
wrote:

> OK. Actually I was wrong, the file has size of 0! I don’t know what
> happened when you installed freesurfer or ran recon-all, but the file was
> not properly written...
>
> On Aug 10, 2017, at 9:34 AM, Z Hessam  wrote:
>
> I copy the *.tar.gz file, and open and install the program by terminal. I
> am confused because that work last week for this data, but now, this
> doesn't work.
> for other datasets, i copy dicom files, then convert them with " recon-all
> -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid
> fat_fh23" command to *.mgz, and then i use the "recon-all -s  -all "
> command in linux terminal.
>
> On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang 
> wrote:
>
>> How did you put the data on your drive?
>>
>> On Aug 10, 2017, at 9:25 AM, Z Hessam  wrote:
>>
>> I didn't copy the file, and drive has 3.7GB free space
>>
>> On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang > > wrote:
>>
>>> Wait, the file size looks too small. Only 1590 bytes. Did the data get
>>> copied properly? Is your drive full?
>>>
>>> On Aug 10, 2017, at 4:40 AM, Z Hessam  wrote:
>>>
>>> it shows:
>>>
>>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 /media/hessam91/driver2/freesu
>>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>>>
>>>
>>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang <
>>> rpw...@nmr.mgh.harvard.edu> wrote:
>>>
 Hmm, if you run:

 ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/be
 rt/mri/T1.mgz

 what does it show?

 On Aug 9, 2017, at 4:47 PM, Z Hessam  wrote:

 of course:

 hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview
 -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz
 bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
 bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red
 bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red

 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
 -1): read error
 MRIread failed: Unable to read from /media/hessam91/driver2/freesu
 rfer/freesurfer/subjects/bert/mri/T1.mgz
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
 -1): read error
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
 -1): read error
 MRIread failed: Unable to read from /media/hessam91/driver2/freesu
 rfer/freesurfer/subjects/bert/mri/T1.mgz
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
 -1): read error

 thanks a lot for your attention

 On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <
 rpw...@nmr.mgh.harvard.edu> wrote:

> Can you copy and paste the exact command line you ran and the error
> message?
>
> Ruopeng
>
>
> On 08/09/2017 02:21 PM, Z Hessam wrote:
>
>
> I try it without \ chars, works for some other subjects
> but it doesn't work for one of them,and now I can even open it with
> GUI, while I could open it before.
> It seems that is time variant!
> Should I run "recon-all ..." again for that subject?
>
>
>
>
> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
>
>> can you try it without all the \ characters?  You shouldn't need them
>> if it's all on one line
>>
>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>
>>
>>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
>>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut
>>> :opacity=0.2
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> MRIread failed: Unable to read from
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>>
>>>
>>> I use the example 4 in the "download and install" page of site
>>>
>>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>>   hmmm, that looks ok, but it's hard to tell with all the
>>>   backslashes and blank lines and such. Can you send the full
>>>   command on a single line (e.g. by hitting up-arrow in the
>>>   terminal window) and the actual output of freeview?
>>>
>>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>>
>>>
>>> Hello Freesurfer Developers,
>>>
>>> I have problem when I use "freeview" example code in
>>> terminal,
>>> freeview -v \
>>>
>>> bert/mri/T1.mgz \
>>>
>>> bert/mri/wm.mgz \
>>>
>>> bert/mri/

[Freesurfer] mri_surf2vol

[Rockers, Elijah D.]

I am attempting to create a volume from a surface. My ultimate goal is to 
obtain a mask that includes everything "inside" the white matter surfaces. 
wm.mgz is close, but it would nicer to just get a mask from lh.white and 
rh.white. I would like these masks to be in the subject's native space. However 
I try the following command and see the resulting error:

mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi lh 
--identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz

gdiagno = -1
Using identity matrix for registration
mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file
mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header

I'm obviously doing something wrong here, but I'm not sure what needs to 
change. I used --identity because native space, and it wouldn't let me run the 
command without specifying --template, which I'm not sure I understand, 
because, again, target is native space. Please illuminate me,

Thank you,

- Eli

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
a Magnet hospital for excellence in nursing.  Visit us at  
houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
facebook.com/HoustonMethodist.  ***CONFIDENTIALITY NOTICE*** This e-mail is the 
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Re: [Freesurfer] Talairach error

[Douglas N Greve]

you can visually check it. Also, it is not super critical


On 08/10/2017 01:45 PM, Yagmur Ozdemir 19 wrote:
> I would prefer to have it run with the tal registration, as I am not entirely 
> sure if the registration works ok as it was made in another software, but 
> worst case I will try that option. Thank you!
>
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 10, 2017 1:18 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Talairach error
>
> It is failing the tal registration check. Does the registration look ok?
> If so, then run with -no-talcheck.
>
>
> On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
>> Hello FreeSurfer experts,
>>
>> I have been running into a consistent problem of Talairach alignment
>> error in my recon-all for some of my subjects, even though I was able
>> to get a completed recon-all for other subjects by using the same
>> procedure to obtain my nifti files. I have attached the recon-all logs
>> of a successful and a Talairach failed subject respectively, and as I
>> try to understand the difference, in the successful one this was tried
>> the last: INFO: Trying MINC mritotal to perform Talairach align...
>> then failed, then there is a "New invocation of recon-all " which
>> succeeded. I do not think I made that invocation. Could someone help
>> me figure out what I am missing, and how can I make recon-all continue
>> as I somehow did previously?
>>
>> Thank you so much!
>> Idil
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Talairach error

[Yagmur Ozdemir 19]

I would prefer to have it run with the tal registration, as I am not entirely 
sure if the registration works ok as it was made in another software, but worst 
case I will try that option. Thank you!

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, August 10, 2017 1:18 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach error

It is failing the tal registration check. Does the registration look ok?
If so, then run with -no-talcheck.


On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
> Hello FreeSurfer experts,
>
> I have been running into a consistent problem of Talairach alignment
> error in my recon-all for some of my subjects, even though I was able
> to get a completed recon-all for other subjects by using the same
> procedure to obtain my nifti files. I have attached the recon-all logs
> of a successful and a Talairach failed subject respectively, and as I
> try to understand the difference, in the successful one this was tried
> the last: INFO: Trying MINC mritotal to perform Talairach align...
> then failed, then there is a "New invocation of recon-all " which
> succeeded. I do not think I made that invocation. Could someone help
> me figure out what I am missing, and how can I make recon-all continue
> as I somehow did previously?
>
> Thank you so much!
> Idil
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Hippocampus subfield segmentation Aborted

[Iglesias Gonzalez, Eugenio]

Dear Vasudev,
I’ve never encountered this problem…
Can you please try this?
https://uk.mathworks.com/matlabcentral/answers/126994-locale-system-error
Cheers,
/Eugenio

From:  on behalf of Dev vasu 

Reply-To: Freesurfer support list 
Date: Thursday, 10 August 2017 at 15:53
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampus subfield segmentation Aborted

Dear all,
I am encountering following error when i run Hippocampus subfield segmentation

"run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266 Aborted   
  "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args ".
I am annexing the log file for your notice please kindly review it and let me 
know why its getting intermittently aborted  .

Thanks
Vasudev
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Re: [Freesurfer] GLM error - cannot read fsgd file for reading

[Douglas N Greve]

y.mgh is the input file, usually the output of mris_preproc (after 
smoothing). See the group analysis tutorial.


On 08/10/2017 11:48 AM, Nick Corriveau-Lecavalier wrote:
>
> Hi Freesurfer team,
>
>
> First, sorry making a new post, I'm having trouble with my email and 
> I'm not able to reply directly on my yesterday's post.
>
>
> Here's my issue: I'm trying to make a group analysis with 3 groups 
> using the mri_glmfit command.
>
>
> This it what the terminal says: Loading y from 
> /Applications/freesurfer/subjects/fsgd/y.mgh
>
> mghRead(/Applications/freesurfer/subjects/fsgd/y.mgh, -1): could not 
> open file
>
> ERROR: loading y /Applications/freesurfer/subjects/fsgd/y.mgh
>
>
> The terminal says that it cannot load the y.mgh file, which seems 
> logic to me, since there is no such file in my folder. What is that 
> file supposed to be? It isn't mentionned in the tutorial I've been 
> following (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V).
>
>
> I also attached the log file.
>
>
> Thank you!
>
>
> FYI, here is my previous discussion with Douglas about this issue:
>
>
> Douglas N Greve 
> 
>  
> Wed, 09 Aug 2017 14:17:05 -0700 
> 
>
> make sure you pass the full path to the fsgd, otherwise it looks in the
> current folder. Also make sure it is readable by you
>
>
> > Hi Freesurfer team,
> >
> >
> > I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) 
> > with 0 covariables at the moment, but I would like to add two 
> > eventually. I've been following the tutorial on this link: 
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write
> > the command it says ''cannot open g3v0.fsgd for reading''.
> >
> >
> > In my /subjects/fsgd file, there is my fsgd file, and my contrast 
> > file. Am I missing an additionnal file or something? Is the format of 
> > my files correct?
> >
> >
> > If it can help, here's what my fsgd file looks likes:
> >
> >
> > GroupDescriptorFile 1
> > Title OSGM
> > Class Control
> > Class SCD
> > Class MCI
> > Variables
> > Input 3431566 CTL
> > Input 3514091 CTL
> > Input 4051959 CTL
> > Input 4344061 CTL
> > Input 4557550 CTL
> > Input 7060373 CTL
> > Input 7274924 CTL
> ETC
>
>
>
> Nick Corriveau-Lecavalier, B.Sc. (Hons)
> Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique
> Coordonateur à la recherche, Association étudiante des cycles 
> supérieurs en psychologie de l'Université de Montréal (AÉCSPUM)
> Université de Montréal
> Centre de recherche de l'Institut universitaire de gériatrie de 
> Montréal, bureau M7819
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] GLM error - cannot read fsgd file for reading

[Nick Corriveau-Lecavalier]

Hi Freesurfer team,


First, sorry making a new post, I'm having trouble with my email and I'm not 
able to reply directly on my yesterday's post.


Here's my issue: I'm trying to make a group analysis with 3 groups using the 
mri_glmfit command.


This it what the terminal says: Loading y from 
/Applications/freesurfer/subjects/fsgd/y.mgh

mghRead(/Applications/freesurfer/subjects/fsgd/y.mgh, -1): could not open file

ERROR: loading y /Applications/freesurfer/subjects/fsgd/y.mgh


The terminal says that it cannot load the y.mgh file, which seems logic to me, 
since there is no such file in my folder. What is that file supposed to be? It 
isn't mentionned in the tutorial I've been following 
(https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V).


I also attached the log file.


Thank you!


FYI, here is my previous discussion with Douglas about this issue:


Douglas N 
Greve
 Wed, 09 Aug 2017 14:17:05 
-0700

make sure you pass the full path to the fsgd, otherwise it looks in the
current folder. Also make sure it is readable by you


> Hi Freesurfer team,
>
>
> I'm trying to run a GLM analysis with three groups (Controls, MCI, AD)
> with 0 covariables at the moment, but I would like to add two
> eventually. I've been following the tutorial on this link:
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write
> the command it says ''cannot open g3v0.fsgd for reading''.
>
>
> In my /subjects/fsgd file, there is my fsgd file, and my contrast
> file. Am I missing an additionnal file or something? Is the format of
> my files correct?
>
>
> If it can help, here's what my fsgd file looks likes:
>
>
> GroupDescriptorFile 1
> Title OSGM
> Class Control
> Class SCD
> Class MCI
> Variables
> Input 3431566 CTL
> Input 3514091 CTL
> Input 4051959 CTL
> Input 4344061 CTL
> Input 4557550 CTL
> Input 7060373 CTL
> Input 7274924 CTL

ETC



Nick Corriveau-Lecavalier, B.Sc. (Hons)
Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur à la recherche, Association étudiante des cycles supérieurs en 
psychologie de l'Université de Montréal (AÉCSPUM)
Université de Montréal
Centre de recherche de l'Institut universitaire de gériatrie de Montréal, 
bureau M7819


mri_glmfit.log
Description: mri_glmfit.log
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Re: [Freesurfer] Linear Mixed Effects model

[Diers, Kersten /DZNE]

Hi Kasper,

your design matrix X should have as many rows as there are measurements. Say if 
you have m subjects with n measurements each, it will be m*n rows. If different 
subjects have different numbers of measurements, that's also OK; in such cases 
the number of rows per subject in X will also differ.

Then, X should contain the following columns:

1. intercept 
this column should be all ones

2. time from baseline
if you have two time-points for each subject, this column should look as 
follows:
0 follow-up-time_subj1 0 follow-up-time_subj2 0 follow-up-time_subj3 etc.
here, follow-up-time is the difference in time between time-point 1 and 2, i.e. 
(time-point 2 minus time-point 1).

3. group indicator
0 for controls, 1 for patients

4. time x group interaction
multiply the values of columns 2 and 3

Further, it is important that the rows of X are ordered according to time for 
each subject. In your case with two measurements for each subject (if I 
understood correctly), this means that for the rows of X, time should be the 
faster changing index, and subject the slower changing index. This results in a 
sequence like subj1_time1 subj1_time2 subj2_time1 subj2_time2 subj3_time1 etc.
Needless to say, this must be the same in the ordering of your data variable Y.

Hope this helps,

Kersten



Am 08.08.2017 um 14:52 schrieb Kasper Jessen :

> Dear FreeSurfer,
> 
> I have a longitudinal study (patients and controls) with two time points 
> (i.e., baseline and six-weeks follow-up). I would like to use the LME model 
> as it can handle unequal timing and different number of time points across 
> subjects due to missing data. 
> 
> I would like to test if there is an effect of (a) time (b) group and (c) 
> group x time interaction.
> 
> However, i am trouble with my design matrix X:
> 
> (1) How would i write X? 
> 
> Thanks in advance
> Best regards
> Kasper
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> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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Re: [Freesurfer] PET surfer

[Douglas N Greve]

On 08/10/2017 11:35 AM, John Anderson wrote:
>
> Dear Dr Greve,
>
> Thank you very much for the great explanation. I will definitely 
> correct for PVC using PET surfer.
>
> Kindly I have one follow-up question and I highly appreciate your input.
>
> I have PET data for two groups. I studied the difference in PET signal 
> using  voxel-wise ( FSL/randomise) and surface-based using PET surfer.
>
> My question is about PVC. We correct for PVC in surface based because 
> we re-sample PET data to the brain surface which is an output of 
> segmentation process, meaning we expect partial volume effects between 
> the grey/white  for a possible contamination between them during 
> segmentation.

>
> We don't do PVE in voxel-wise because we don't worry about the 
> contamination meaning there are no segmentation lines to separate 
> between brain regions.

>
> Kindly is my understanding for this fact correct ( i.e. why we correct 
> in surface based and we don't correct in voxel-wise).
It is not correct. You do PVC to remove interactions between the anatomy 
and the PET through PVEs. Those will be there in both surface-based and 
volume-based analysis.  If you perform smoothing in volume-based 
analysis, you will make the PVEs worse. Doing MG PVC then volume-based 
smoothing will result in a disaster. In my opinion, the only way to do 
PVC in a map-based analysis (vs ROI) is to do it on the surface. For 
subcortical, you can do volume-based smoothing within a GM mask.

> By the way, I ran voxel-wise using randomise with TFCE and 5000 
> permutations.
For the surface, you can use mri_glmfit with the --perm option.
>
> Thank you again for any clarification
> John
>
>
>
>
> The PET signalcan change with a lot of anatomical changes in the brain 
> including thickness, surface area, and gyrification. There is no known 
> regressor that will account for this. Right right way to account for 
> it is with partialvolume correction (PVC). It is best to do PVC 
> simultaneously with the recon, but software is not available to 
> perform this. You can do it on a post-hoc basis in PETsurfer using the 
> PVC options in mri_gtmpvc. See the wiki.
>
>
>
> On 08/10/2017 04:11 AM, John Anderson wrote:
>
> >
>
> > Hi Dr Greve,
>
> >
>
> > I have PET data for two groups and I used PET surfer in FSV 6.0 to run
>
> > the analyses. The pipeline is straightforward and the analysis ran
>
> > smoothly without any issues.
>
> >
>
> > Is it correct procedure to adjust PET signal to differences in gray
>
> > matter volume or cortical thinness between two groups?
>
> >
>
> > In other words, is it correct if gray matter volume or cortical
>
> > thickness for subjects be included as EVs in GLM or a nausiance factor
>
> > in QDEC?
>
> >
>
> > Specifically, is the PET signal changeable depending ondifferences
>
> > in cortical thickness.
>
> > or differences in gray matter volume?
>
> >
>
> > Thank youfor any clarification
>
> >
>
> >> Thank you !
>
> >> Jon
>
> >>
>
> >
>
> >
>
> >
>
> > ___
>
> > Freesurfer mailing list
>
> > Freesurfer@nmr.mgh.harvard.edu 
>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
>
> Douglas N. Greve, Ph.D.
>
> MGH-NMR Center
>
> gr...@nmr.mgh.harvard.edu 
>
> Phone Number: 617-724-2358
>
> Fax: 617-726-7422
>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu 
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer /A��J2�
>
>>  Original Message 
>> Subject: PET surfer
>> Local Time: August 10, 2017 4:11 AM
>> UTC Time: August 10, 2017 8:11 AM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list 
>>
>> Hi Dr Greve,
>>
>> I have PET data for two groups and I used PET surfer in FSV 6.0 to 
>> run the analyses. The pipeline is straightforward and the analysis 
>> ran smoothly without any issues.
>>
>> Is it correct procedure to adjust PET signal to differences in gray 
>> matter volume or cortical thinness between two groups?
>>
>> In other words, is it correct if gray matter volume or cortical 
>> thickness for subjects be included as EVs in GLM or a nausiance 
>> factor in QDEC?
>>
>> Specifically, is the PET signal changeable depending on  differences 
>> in cortical thickness.
>> or differences in gray matter volume?
>>
>> Thank you  for any clarification
>>
>>> Thank you !
>>> Jon
>>>
>>
>
>
>
> ___
> Freesurfer mailing li

Re: [Freesurfer] PET surfer

[John Anderson]

Dear Dr Greve,

Thank you very much for the great explanation. I will definitely correct for 
PVC using PET surfer.

Kindly I have one follow-up question and I highly appreciate your input.

I have PET data for two groups. I studied the difference in PET signal using  
voxel-wise ( FSL/randomise) and surface-based using PET surfer.

My question is about PVC. We correct for PVC in surface based because we 
re-sample PET data to the brain surface which is an output of segmentation 
process, meaning we expect partial volume effects between the grey/white  for a 
possible contamination between them during segmentation.

We don't do PVE in voxel-wise because we don't worry about the contamination 
meaning there are no segmentation lines to separate between brain regions.

Kindly is my understanding for this fact correct ( i.e. why we correct in 
surface based and we don't correct in voxel-wise). By the way, I ran voxel-wise 
using randomise with TFCE and 5000 permutations.

Thank you again for any clarification
John

The PET signal  can change with a lot of anatomical changes in the brain 
including thickness, surface area, and gyrification. There is no known 
regressor that will account for this. Right right way to account for it is with 
partial  volume correction (PVC). It is best to do PVC simultaneously with the 
recon, but software is not available to perform this. You can do it on a 
post-hoc basis in PETsurfer using the PVC options in mri_gtmpvc. See the wiki.

On 08/10/2017 04:11 AM, John Anderson wrote:

>

> Hi Dr Greve,

>

> I have PET data for two groups and I used PET surfer in FSV 6.0 to run

> the analyses. The pipeline is straightforward and the analysis ran

> smoothly without any issues.

>

> Is it correct procedure to adjust PET signal to differences in gray

> matter volume or cortical thinness between two groups?

>

> In other words, is it correct if gray matter volume or cortical

> thickness for subjects be included as EVs in GLM or a nausiance factor

> in QDEC?

>

> Specifically, is the PET signal changeable depending on  differences

> in cortical thickness.

> or differences in gray matter volume?

>

> Thank you  for any clarification

>

>> Thank you !

>> Jon

>>

>

>

>

> ___

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Douglas N. Greve, Ph.D.

MGH-NMR Center

gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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>  Original Message 
> Subject: PET surfer
> Local Time: August 10, 2017 4:11 AM
> UTC Time: August 10, 2017 8:11 AM
> From: john.ande...@protonmail.com
> To: Freesurfer support list 
>
> Hi Dr Greve,
>
> I have PET data for two groups and I used PET surfer in FSV 6.0 to run the 
> analyses. The pipeline is straightforward and the analysis ran smoothly 
> without any issues.
>
> Is it correct procedure to adjust PET signal to differences in gray matter 
> volume or cortical thinness between two groups?
>
> In other words, is it correct if gray matter volume or cortical thickness for 
> subjects be included as EVs in GLM or a nausiance factor in QDEC?
>
> Specifically, is the PET signal changeable depending on  differences in 
> cortical thickness.
> or differences in gray matter volume?
>
> Thank you  for any clarification
>
>> Thank you !
>> Jon___
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Re: [Freesurfer] Cortical thickness map for a pediatric case

[Sneha Pandya]

Hi Bruce and Martin,


Wanted to follow up and see if you'll got a chance to look at the error and if 
I could try out something?


Thanks,

Sneha


From: Sneha Pandya
Sent: Tuesday, August 8, 2017 11:29:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case


Thank you Bruce, sure thing :)


Regards,

Sneha


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, August 7, 2017 6:21:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case

thanks Sneha

you'll probably need to wait until tomorrow for Martin to read his email :)

cheers
Bruce

On Mon, 7 Aug 2017, Sneha Pandya wrote:

>
> Hi Bruce,
>
>
> Sure, please see highlighted below part of screen output showing the error.
> Since I ran the command within a screen sesison I have saved executed screen
> session to a log file. Find attached log file with output of entire run. 
> Please
> let me know if any other files are required and if attached log file could be
> interpreted.
>
>
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_0.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_1_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_1.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_1.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_2_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_2.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_2.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_3_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_3.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_3.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_4_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_4.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_4.lta...
> mri_concatenate_lta successful.
> #
> #@# MotionCor Wed Jul 26 14:04:13 EDT 2017
>
>  mri_add_xform_to_header -c
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/talairach.xfm
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz
>
> INFO: extension is mgz
> #
> #@# Talairach Wed Jul 26 14:04:14 EDT 2017
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
> Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 
> x86_64
> x86_64 x86_64 GNU/Linux
>
> recon-all -s ped1_base exited with ERRORS at Wed Jul 26 14:04:17 EDT 2017
>
> For more details, see the log file
> /shared_data2/sneha/MSKCC_Processed/ped1_base/scripts/recon-all.log
> To report a problem, see 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=DwIDbA&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=BoRZLsXqqVT6-Qe8baTB-uaC5VkO8MylpF2Pge0ejiI&s=80fR0T3L4F8R5icMg6uqKyEXyWyEbcpI5AFOF2UVRzo&e=
>
>
> Thanks,
>
> Sneha
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: Monday, August 7, 2017 2:02:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
> Hi Sneha
>
> can you include the output as text instead of an image?
>
> thanks
> Bruce
> On Mon, 7 Aug 2017,
> Sneha Pandya wrote:
>
> >
> > Hi Bruce,
> >
> >
> > Please find attached recon-all.log file and I used following command to run
> the base:
> >
> >
> > recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3 -tp
> ped1_4 -all
> >
> >
> > Following is the screen shot of output showing the error:
> >
> > [IMAGE]
> >
> > Thanks,
> > Sneha
> >
> >__
> __
> 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> > Sent: Monday, August 7, 2017 1:43:01 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
> > Hi Sneha
> >
> > can you send us the commad you ran and the full screen output inluding
> > the error and also the recon-all.log?
> >
> > cheers
> > Bruce
> >
> > On Mon, 7
> > Aug 2017, Sneha Pandya wrote:
> >
> > >
> > > Dear team,
> > >
> > >
> > > I have completed cross-sectional pipeline on my pediatric 

Re: [Freesurfer] Reporting age differences between groups

[Douglas N Greve]

I would report it. Just using an age regressor is not guaranteed to 
remove all age effects. This does not invalidate your study, but it 
should be mentioned.


On 08/09/2017 10:43 PM, Martin Juneja wrote:
> Hi,
>
> I need a general advice from the experts out there.
>
> I am comparing cortical measures (thickness and volume) between 
> controls and patients using FreeSurfer. I used 'age' and 'gender' as 
> covariates (in fsgd file) while calculating group differences.
>
> I was wondering even if I removed the effects of 'age' and 'gender' 
> for this comparison, should I perform and report t-test/one way ANOVA 
> results if there are significant differences in 'age' between the two 
> groups or there is no need to report 'age' difference results in 
> manuscript, regardless of being significant or non-significant.
>
> Thanks.
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Hippocampus subfield segmentation Aborted

[Dev vasu]

Dear all,

I am encountering following error when i run Hippocampus subfield
segmentation

"run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266
Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML
$args ".

I am annexing the log file for your notice please kindly review it and let
me know why its getting intermittently aborted  .


Thanks
Vasudev
#
#@# Hippocampal Subfields processing (T1 only) left Fri Jul 21 13:57:20 EDT 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/runtime/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/bin/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/os/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/project/m/mchakrav/quarantine/ANTs/git/build/lib:/scinet/gpc/Libraries/zlib-1.2.8/lib:/scinet/gpc/tools/Python/Python272-shared/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/ipp/lib/intel64:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/tbb/lib/intel64:/scinet/gpc/compilers/gcc-5.2.0/requiredlibs/lib:/scinet/gpc/compilers/gcc-5.2.0/lib:/scinet/gpc/compilers/gcc-5.2.0/lib64:/scinet/gpc/lib64_6.4:/scinet/gpc/lib64_6.4/mysql:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/scinet/gpc/intel/debugger_2016/libipt/intel64/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64
terminate called after throwing an instance of 'std::runtime_error'
  what():  locale::facet::_S_create_c_locale name not valid
/sgfs1/scratch3/m/mchakrav/vasudev/freesurfer/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
#
#@# Hippocampal Subfields processing (T1 only) right Fri Jul 21 13:57:20 EDT 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/runtime/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/bin/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/os/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/project/m/mchakrav/quarantine/ANTs/git/build/lib:/scinet/gpc/Libraries/zlib-1.2.8/lib:/scinet/gpc/tools/Python/Python272-shared/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/ipp/lib/intel64:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/tbb/lib/intel64:/scinet/gpc/compilers/gcc-5.2.0/requiredlibs/lib:/scinet/gpc/compilers/gcc-5.2.0/lib:/scinet/gpc/compilers/gcc-5.2.0/lib64:/scinet/gpc/lib64_6.4:/scinet/gpc/lib64_6.4/mysql:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/scinet/gpc/intel/debugger_2016/libipt/intel64/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64
terminate called after throwing an instance of 'std::runtime_error'
  what():  locale::facet::_S_create_c_locale name not valid
/sgfs1/scratch3/m/mchakrav/vasudev/freesurfer/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11332 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
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Re: [Freesurfer] Hippocampus subfield

[Iman Aganj]

Hi Ariel,

I second Bruce; we don't have a pipeline to directly measure the subfield
thickness. We have, however, tried an indirect volumetric method to compute
the thickness (http://nmr.mgh.harvard.edu/~koen/IglesiasNI2014.pdf, the
"Experimental setup" section). It requires a (preferably soft) segmentation
of each subfield, parameter tuning, and skeleton computation for reading the
thickness values. So if you're willing to try it in spite of it not being so
straightforward, I'm happy to share the tissue thickness measurement codes.

Best,
Iman

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, August 10, 2017 10:26 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampus subfield

no, not really

sorry
Bruce
On Thu, 10 Aug 2017, Lin, Yizhi wrote:

> Dear experts in Freesurfer,
> I am doing analysis on hippocampus subfield and I'm wondering if I 
> could obtain cortical thickness data from each segmentation? Thanks so
much!
> 
> Best,
> 
> Ariel
> 
>
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Re: [Freesurfer] PET surfer

[Douglas N Greve]

The PET signal  can change with a lot of anatomical changes in the brain 
including thickness, surface area, and gyrification. There is no known 
regressor that will account for this. Right right way to account for it 
is with partial  volume correction (PVC). It is best to do PVC 
simultaneously with the recon, but software is not available to perform 
this. You can do it on a post-hoc basis in PETsurfer using the PVC 
options in mri_gtmpvc. See the wiki.


On 08/10/2017 04:11 AM, John Anderson wrote:
>
> Hi Dr Greve,
>
> I have PET data for two groups and I used PET surfer in FSV 6.0 to run 
> the analyses. The pipeline is straightforward and the analysis ran 
> smoothly without any issues.
>
> Is it correct procedure to adjust PET signal to differences in gray 
> matter volume or cortical thinness between two groups?
>
> In other words, is it correct if gray matter volume or cortical 
> thickness for subjects be included as EVs in GLM or a nausiance factor 
> in QDEC?
>
> Specifically, is the PET signal changeable depending on  differences 
> in cortical thickness.
> or differences in gray matter volume?
>
> Thank you  for any clarification
>
>> Thank you !
>> Jon
>>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Freesurfer PIB PET image processing

[Douglas N Greve]

do you mean to run the anatomical analysis on them? No.


On 08/10/2017 05:23 AM, M Janani wrote:
> Is it correct to process the PiB images using Freesurfer ?
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 10 August 2017 03:41
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>
> We do not have any thing to specifically analyze PiB. You can look at the 
> PETsurfer page for more general instructions
>
>
> On 08/09/2017 02:15 AM, M Janani wrote:
>> Hi Team,
>>
>> I apologize, I am new to Freesurfer.
>>
>> Currently we are processing PIB PET images.
>>
>>  When we compare the SPM data along with FREESURFER
>> outputs. We were able to see a large variation in the values.
>>
>>  Could you please guide us in processing PIB PET images
>> in Freesurfer?
>>
>>  Since the signal of a PET image is very weak, we used
>> MRI image as a guide to map it to Standard brain.
>>
>>  How does Freesurfer process in this case?
>>
>>  Your help would be grateful.
>>
>> Regards,
>>
>> Janani
>>
>>
>>
>> ::DISCLAIMER::
>> 
>>
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>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Hippocampus subfield

[Bruce Fischl]

no, not really

sorry
Bruce
On Thu, 10 Aug 2017, Lin, Yizhi wrote:

> Dear experts in Freesurfer,
> I am doing analysis on hippocampus subfield and I'm wondering if I could
> obtain cortical thickness data from each segmentation? Thanks so much!
> 
> Best,
> 
> Ariel
> 
>
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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

OK. Actually I was wrong, the file has size of 0! I don’t know what happened 
when you installed freesurfer or ran recon-all, but the file was not properly 
written...

> On Aug 10, 2017, at 9:34 AM, Z Hessam  wrote:
> 
> I copy the *.tar.gz file, and open and install the program by terminal. I am 
> confused because that work last week for this data, but now, this doesn't 
> work.
> for other datasets, i copy dicom files, then convert them with " recon-all -i 
> STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 
> fat_fh23" command to *.mgz, and then i use the "recon-all -s  -all " 
> command in linux terminal.
> 
> On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang  > wrote:
> How did you put the data on your drive?
> 
>> On Aug 10, 2017, at 9:25 AM, Z Hessam > > wrote:
>> 
>> I didn't copy the file, and drive has 3.7GB free space
>> 
>> On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang > > wrote:
>> Wait, the file size looks too small. Only 1590 bytes. Did the data get 
>> copied properly? Is your drive full? 
>> 
>>> On Aug 10, 2017, at 4:40 AM, Z Hessam >> > wrote:
>>> 
>>> it shows:
>>> 
>>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> 
>>> 
>>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang >> > wrote:
>>> Hmm, if you run:
>>> 
>>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> 
>>> what does it show?
>>> 
 On Aug 9, 2017, at 4:47 PM, Z Hessam >>> > wrote:
 
 of course:
 
 hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
 bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
 bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
 bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
 bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
 
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
  -1): read error
 MRIread failed: Unable to read from 
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
  -1): read error
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
  -1): read error
 MRIread failed: Unable to read from 
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
 mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
  -1): read error
 
 thanks a lot for your attention 
 
 On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang >>> > wrote:
 Can you copy and paste the exact command line you ran and the error 
 message?
 
 Ruopeng
 
 
 On 08/09/2017 02:21 PM, Z Hessam wrote:
> 
> I try it without \ chars, works for some other subjects
> but it doesn't work for one of them,and now I can even open it with GUI, 
> while I could open it before.
> It seems that is time variant!
> Should I run "recon-all ..." again for that subject?
> 
> 
> 
> 
> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl  > wrote:
> can you try it without all the \ characters?  You shouldn't need them if 
> it's all on one line
> 
> On Wed, 9 Aug 2017, Z Hessam wrote:
> 
> 
> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
> mri_read(): couldn't determine type of file
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> MRIread failed: Unable to read from
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> mri_read(): couldn't determine type of file
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> 
> 
> I use the example 4 in the "download and install" page of site
> 
> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl  >
> wrote:
> 
>   hmmm, that looks ok, but it's hard to tell with all the
>   backslashes and blank lines and such. Can you send the full
>   command on a single line (e.g. by hitting up-arrow in the
>   terminal window) and the actual output of freeview?
> 
>On Wed, 9 Aug 2017, Z Hessam wrote:
> 
> 
> Hello Freesurfer Developers,
> 
> I have problem when I use "freeview" example code in
> terminal,
> freeview -v \
> 
> bert/mri/T1.mgz \
> 
> bert/mri/wm.mgz \
> 
> bert/mri/brainmask

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

I copy the *.tar.gz file, and open and install the program by terminal. I
am confused because that work last week for this data, but now, this
doesn't work.
for other datasets, i copy dicom files, then convert them with " recon-all
-i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid
fat_fh23" command to *.mgz, and then i use the "recon-all -s  -all "
command in linux terminal.

On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang 
wrote:

> How did you put the data on your drive?
>
> On Aug 10, 2017, at 9:25 AM, Z Hessam  wrote:
>
> I didn't copy the file, and drive has 3.7GB free space
>
> On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang 
> wrote:
>
>> Wait, the file size looks too small. Only 1590 bytes. Did the data get
>> copied properly? Is your drive full?
>>
>> On Aug 10, 2017, at 4:40 AM, Z Hessam  wrote:
>>
>> it shows:
>>
>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 /media/hessam91/driver2/freesu
>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>>
>>
>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang > > wrote:
>>
>>> Hmm, if you run:
>>>
>>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/be
>>> rt/mri/T1.mgz
>>>
>>> what does it show?
>>>
>>> On Aug 9, 2017, at 4:47 PM, Z Hessam  wrote:
>>>
>>> of course:
>>>
>>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview
>>> -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
>>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red
>>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>>
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>> -1): read error
>>> MRIread failed: Unable to read from /media/hessam91/driver2/freesu
>>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>> -1): read error
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>> -1): read error
>>> MRIread failed: Unable to read from /media/hessam91/driver2/freesu
>>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>> -1): read error
>>>
>>> thanks a lot for your attention
>>>
>>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <
>>> rpw...@nmr.mgh.harvard.edu> wrote:
>>>
 Can you copy and paste the exact command line you ran and the error
 message?

 Ruopeng


 On 08/09/2017 02:21 PM, Z Hessam wrote:


 I try it without \ chars, works for some other subjects
 but it doesn't work for one of them,and now I can even open it with
 GUI, while I could open it before.
 It seems that is time variant!
 Should I run "recon-all ..." again for that subject?




 On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <
 fis...@nmr.mgh.harvard.edu> wrote:

> can you try it without all the \ characters?  You shouldn't need them
> if it's all on one line
>
> On Wed, 9 Aug 2017, Z Hessam wrote:
>
>
>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut
>> :opacity=0.2
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> MRIread failed: Unable to read from
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>
>>
>> I use the example 4 in the "download and install" page of site
>>
>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   hmmm, that looks ok, but it's hard to tell with all the
>>   backslashes and blank lines and such. Can you send the full
>>   command on a single line (e.g. by hitting up-arrow in the
>>   terminal window) and the actual output of freeview?
>>
>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>
>>
>> Hello Freesurfer Developers,
>>
>> I have problem when I use "freeview" example code in
>> terminal,
>> freeview -v \
>>
>> bert/mri/T1.mgz \
>>
>> bert/mri/wm.mgz \
>>
>> bert/mri/brainmask.mgz \
>>
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>
>> -f \
>>
>> bert/surf/lh.white:edgecolor=blue \
>>
>> bert/surf/lh.pial:edgecolor=red \
>>
>> bert/surf/rh.white:edgecolor=blue \
>>
>> bert/surf/rh.pial:edgecolor=red
>> it tell "Failed to load MRI ",
>> mri_read(): couldn't determine type of file
>> 

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

How did you put the data on your drive?

> On Aug 10, 2017, at 9:25 AM, Z Hessam  wrote:
> 
> I didn't copy the file, and drive has 3.7GB free space
> 
> On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang  > wrote:
> Wait, the file size looks too small. Only 1590 bytes. Did the data get copied 
> properly? Is your drive full? 
> 
>> On Aug 10, 2017, at 4:40 AM, Z Hessam > > wrote:
>> 
>> it shows:
>> 
>> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> 
>> 
>> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang > > wrote:
>> Hmm, if you run:
>> 
>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> 
>> what does it show?
>> 
>>> On Aug 9, 2017, at 4:47 PM, Z Hessam >> > wrote:
>>> 
>>> of course:
>>> 
>>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
>>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
>>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
>>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>> 
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> MRIread failed: Unable to read from 
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> MRIread failed: Unable to read from 
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>>  -1): read error
>>> 
>>> thanks a lot for your attention 
>>> 
>>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang >> > wrote:
>>> Can you copy and paste the exact command line you ran and the error message?
>>> 
>>> Ruopeng
>>> 
>>> 
>>> On 08/09/2017 02:21 PM, Z Hessam wrote:
 
 I try it without \ chars, works for some other subjects
 but it doesn't work for one of them,and now I can even open it with GUI, 
 while I could open it before.
 It seems that is time variant!
 Should I run "recon-all ..." again for that subject?
 
 
 
 
 On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl >>> > wrote:
 can you try it without all the \ characters?  You shouldn't need them if 
 it's all on one line
 
 On Wed, 9 Aug 2017, Z Hessam wrote:
 
 
 $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
 bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
 mri_read(): couldn't determine type of file
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/
 MRIread failed: Unable to read from
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/
 mri_read(): couldn't determine type of file
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/
 
 
 I use the example 4 in the "download and install" page of site
 
 On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl >>> >
 wrote:
 
   hmmm, that looks ok, but it's hard to tell with all the
   backslashes and blank lines and such. Can you send the full
   command on a single line (e.g. by hitting up-arrow in the
   terminal window) and the actual output of freeview?
 
On Wed, 9 Aug 2017, Z Hessam wrote:
 
 
 Hello Freesurfer Developers,
 
 I have problem when I use "freeview" example code in
 terminal,
 freeview -v \
 
 bert/mri/T1.mgz \
 
 bert/mri/wm.mgz \
 
 bert/mri/brainmask.mgz \
 

 bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
 
 -f \
 
 bert/surf/lh.white:edgecolor=blue \
 
 bert/surf/lh.pial:edgecolor=red \
 
 bert/surf/rh.white:edgecolor=blue \
 
 bert/surf/rh.pial:edgecolor=red
 it tell "Failed to load MRI ",
 mri_read(): couldn't determine type of file
 
 MRIread failed: Unable to read from 
 mri_read(): couldn't determine type of file
 
 but i can load wm.mgz and other existed files in
 GUI.
 
 please help me to know why this error happend? and
 what should I do to solve
  this?
 
 I'

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

I didn't copy the file, and drive has 3.7GB free space

On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang 
wrote:

> Wait, the file size looks too small. Only 1590 bytes. Did the data get
> copied properly? Is your drive full?
>
> On Aug 10, 2017, at 4:40 AM, Z Hessam  wrote:
>
> it shows:
>
> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 /media/hessam91/driver2/
> freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>
>
> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang 
> wrote:
>
>> Hmm, if you run:
>>
>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> bert/mri/T1.mgz
>>
>> what does it show?
>>
>> On Aug 9, 2017, at 4:47 PM, Z Hessam  wrote:
>>
>> of course:
>>
>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v
>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red
>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>> MRIread failed: Unable to read from /media/hessam91/driver2/freesu
>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>> MRIread failed: Unable to read from /media/hessam91/driver2/freesu
>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>>
>> thanks a lot for your attention
>>
>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang > > wrote:
>>
>>> Can you copy and paste the exact command line you ran and the error
>>> message?
>>>
>>> Ruopeng
>>>
>>>
>>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>>
>>>
>>> I try it without \ chars, works for some other subjects
>>> but it doesn't work for one of them,and now I can even open it with GUI,
>>> while I could open it before.
>>> It seems that is time variant!
>>> Should I run "recon-all ..." again for that subject?
>>>
>>>
>>>
>>>
>>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>>
 can you try it without all the \ characters?  You shouldn't need them
 if it's all on one line

 On Wed, 9 Aug 2017, Z Hessam wrote:


> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
> mri_read(): couldn't determine type of file
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> MRIread failed: Unable to read from
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> mri_read(): couldn't determine type of file
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>
>
> I use the example 4 in the "download and install" page of site
>
> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> wrote:
>
>   hmmm, that looks ok, but it's hard to tell with all the
>   backslashes and blank lines and such. Can you send the full
>   command on a single line (e.g. by hitting up-arrow in the
>   terminal window) and the actual output of freeview?
>
>On Wed, 9 Aug 2017, Z Hessam wrote:
>
>
> Hello Freesurfer Developers,
>
> I have problem when I use "freeview" example code in
> terminal,
> freeview -v \
>
> bert/mri/T1.mgz \
>
> bert/mri/wm.mgz \
>
> bert/mri/brainmask.mgz \
>
>
> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>
> -f \
>
> bert/surf/lh.white:edgecolor=blue \
>
> bert/surf/lh.pial:edgecolor=red \
>
> bert/surf/rh.white:edgecolor=blue \
>
> bert/surf/rh.pial:edgecolor=red
> it tell "Failed to load MRI ",
> mri_read(): couldn't determine type of file
> 
> MRIread failed: Unable to read from 
> mri_read(): couldn't determine type of file
> 
> but i can load wm.mgz and other existed files in
> GUI.
>
> please help me to know why this error happend? and
> what should I do to solve
>  this?
>
> I've searched the list, I found a similar errors,
> but wasn't helpful answer reported.
> help me please
>
> regards
>
> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>  wrote:
>
> Hello Freesurfer Developers,
>
>

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

Wait, the file size looks too small. Only 1590 bytes. Did the data get copied 
properly? Is your drive full? 

> On Aug 10, 2017, at 4:40 AM, Z Hessam  wrote:
> 
> it shows:
> 
> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> 
> 
> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang  > wrote:
> Hmm, if you run:
> 
> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> 
> what does it show?
> 
>> On Aug 9, 2017, at 4:47 PM, Z Hessam > > wrote:
>> 
>> of course:
>> 
>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>> 
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> MRIread failed: Unable to read from 
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> MRIread failed: Unable to read from 
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> 
>> thanks a lot for your attention 
>> 
>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang > > wrote:
>> Can you copy and paste the exact command line you ran and the error message?
>> 
>> Ruopeng
>> 
>> 
>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>> 
>>> I try it without \ chars, works for some other subjects
>>> but it doesn't work for one of them,and now I can even open it with GUI, 
>>> while I could open it before.
>>> It seems that is time variant!
>>> Should I run "recon-all ..." again for that subject?
>>> 
>>> 
>>> 
>>> 
>>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl >> > wrote:
>>> can you try it without all the \ characters?  You shouldn't need them if 
>>> it's all on one line
>>> 
>>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>> 
>>> 
>>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
>>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> MRIread failed: Unable to read from
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> 
>>> 
>>> I use the example 4 in the "download and install" page of site
>>> 
>>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl >> >
>>> wrote:
>>> 
>>>   hmmm, that looks ok, but it's hard to tell with all the
>>>   backslashes and blank lines and such. Can you send the full
>>>   command on a single line (e.g. by hitting up-arrow in the
>>>   terminal window) and the actual output of freeview?
>>> 
>>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>> 
>>> 
>>> Hello Freesurfer Developers,
>>> 
>>> I have problem when I use "freeview" example code in
>>> terminal,
>>> freeview -v \
>>> 
>>> bert/mri/T1.mgz \
>>> 
>>> bert/mri/wm.mgz \
>>> 
>>> bert/mri/brainmask.mgz \
>>> 
>>>
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>> 
>>> -f \
>>> 
>>> bert/surf/lh.white:edgecolor=blue \
>>> 
>>> bert/surf/lh.pial:edgecolor=red \
>>> 
>>> bert/surf/rh.white:edgecolor=blue \
>>> 
>>> bert/surf/rh.pial:edgecolor=red
>>> it tell "Failed to load MRI ",
>>> mri_read(): couldn't determine type of file
>>> 
>>> MRIread failed: Unable to read from 
>>> mri_read(): couldn't determine type of file
>>> 
>>> but i can load wm.mgz and other existed files in
>>> GUI.
>>> 
>>> please help me to know why this error happend? and
>>> what should I do to solve
>>>  this?
>>> 
>>> I've searched the list, I found a similar errors,
>>> but wasn't helpful answer reported.
>>> help me please
>>> 
>>> regards
>>> 
>>> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>>> mailto:z.hes...@gmail.com>> wrote:
>>> 
>>> Hello Freesurfer Developers,
>>> 
>>> I have problem when I use "freeview" example code in
>>>   

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

again that error, it shows:

mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
-1): read error
MRIread failed: Unable to read from
/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
-1): read error


On Thu, Aug 10, 2017 at 5:19 PM, Ruopeng Wang 
wrote:

> What if you run:
>
> freeview -v  /media/hessam91/driver2/freesurfer/freesurfer/
> subjects/bert/mri/T1.mgz
>
>
> On Aug 10, 2017, at 4:40 AM, Z Hessam  wrote:
>
> it shows:
>
> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 /media/hessam91/driver2/
> freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>
>
> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang 
> wrote:
>
>> Hmm, if you run:
>>
>> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> bert/mri/T1.mgz
>>
>> what does it show?
>>
>> On Aug 9, 2017, at 4:47 PM, Z Hessam  wrote:
>>
>> of course:
>>
>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v
>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red
>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>>
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>> MRIread failed: Unable to read from /media/hessam91/driver2/freesu
>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>> MRIread failed: Unable to read from /media/hessam91/driver2/freesu
>> rfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>> -1): read error
>>
>> thanks a lot for your attention
>>
>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang > > wrote:
>>
>>> Can you copy and paste the exact command line you ran and the error
>>> message?
>>>
>>> Ruopeng
>>>
>>>
>>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>>
>>>
>>> I try it without \ chars, works for some other subjects
>>> but it doesn't work for one of them,and now I can even open it with GUI,
>>> while I could open it before.
>>> It seems that is time variant!
>>> Should I run "recon-all ..." again for that subject?
>>>
>>>
>>>
>>>
>>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>>
 can you try it without all the \ characters?  You shouldn't need them
 if it's all on one line

 On Wed, 9 Aug 2017, Z Hessam wrote:


> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
> mri_read(): couldn't determine type of file
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> MRIread failed: Unable to read from
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
> mri_read(): couldn't determine type of file
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>
>
> I use the example 4 in the "download and install" page of site
>
> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> wrote:
>
>   hmmm, that looks ok, but it's hard to tell with all the
>   backslashes and blank lines and such. Can you send the full
>   command on a single line (e.g. by hitting up-arrow in the
>   terminal window) and the actual output of freeview?
>
>On Wed, 9 Aug 2017, Z Hessam wrote:
>
>
> Hello Freesurfer Developers,
>
> I have problem when I use "freeview" example code in
> terminal,
> freeview -v \
>
> bert/mri/T1.mgz \
>
> bert/mri/wm.mgz \
>
> bert/mri/brainmask.mgz \
>
>
> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>
> -f \
>
> bert/surf/lh.white:edgecolor=blue \
>
> bert/surf/lh.pial:edgecolor=red \
>
> bert/surf/rh.white:edgecolor=blue \
>
> bert/surf/rh.pial:edgecolor=red
> it tell "Failed to load MRI ",
> mri_read(): couldn't determine type of file
> 
> MRIread failed: Unable to read from 
> mri_read(): couldn't determine type of file
> 
> but i can load wm.mgz and other existed files in
> GUI.
>
> please help me to know why this error happend? and
> what should I do to solve
>  this?
>
> I've searched the list, I found a similar errors,
>   

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Ruopeng Wang]

What if you run:

freeview -v  
/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz


> On Aug 10, 2017, at 4:40 AM, Z Hessam  wrote:
> 
> it shows:
> 
> -rwxrwxrwx 1 8481 1590 0 Aug  9 22:30 
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> 
> 
> On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang  > wrote:
> Hmm, if you run:
> 
> ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> 
> what does it show?
> 
>> On Aug 9, 2017, at 4:47 PM, Z Hessam > > wrote:
>> 
>> of course:
>> 
>> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
>> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
>> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
>> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>> 
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> MRIread failed: Unable to read from 
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> MRIread failed: Unable to read from 
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
>> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>>  -1): read error
>> 
>> thanks a lot for your attention 
>> 
>> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang > > wrote:
>> Can you copy and paste the exact command line you ran and the error message?
>> 
>> Ruopeng
>> 
>> 
>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>> 
>>> I try it without \ chars, works for some other subjects
>>> but it doesn't work for one of them,and now I can even open it with GUI, 
>>> while I could open it before.
>>> It seems that is time variant!
>>> Should I run "recon-all ..." again for that subject?
>>> 
>>> 
>>> 
>>> 
>>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl >> > wrote:
>>> can you try it without all the \ characters?  You shouldn't need them if 
>>> it's all on one line
>>> 
>>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>> 
>>> 
>>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
>>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> MRIread failed: Unable to read from
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> 
>>> 
>>> I use the example 4 in the "download and install" page of site
>>> 
>>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl >> >
>>> wrote:
>>> 
>>>   hmmm, that looks ok, but it's hard to tell with all the
>>>   backslashes and blank lines and such. Can you send the full
>>>   command on a single line (e.g. by hitting up-arrow in the
>>>   terminal window) and the actual output of freeview?
>>> 
>>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>> 
>>> 
>>> Hello Freesurfer Developers,
>>> 
>>> I have problem when I use "freeview" example code in
>>> terminal,
>>> freeview -v \
>>> 
>>> bert/mri/T1.mgz \
>>> 
>>> bert/mri/wm.mgz \
>>> 
>>> bert/mri/brainmask.mgz \
>>> 
>>>
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>> 
>>> -f \
>>> 
>>> bert/surf/lh.white:edgecolor=blue \
>>> 
>>> bert/surf/lh.pial:edgecolor=red \
>>> 
>>> bert/surf/rh.white:edgecolor=blue \
>>> 
>>> bert/surf/rh.pial:edgecolor=red
>>> it tell "Failed to load MRI ",
>>> mri_read(): couldn't determine type of file
>>> 
>>> MRIread failed: Unable to read from 
>>> mri_read(): couldn't determine type of file
>>> 
>>> but i can load wm.mgz and other existed files in
>>> GUI.
>>> 
>>> please help me to know why this error happend? and
>>> what should I do to solve
>>>  this?
>>> 
>>> I've searched the list, I found a similar errors,
>>> but wasn't helpful answer reported.
>>> help me please
>>> 
>>> regards
>>> 
>>> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>>> mailto:z.hes...@gmail.com>> wrote:
>>> 
>>> Hello Freesurfer Developers,
>>> 
>>> I have problem when I use "freeview" example code in
>>> term

Re: [Freesurfer] Freesurfer PIB PET image processing

[M Janani]

Is it correct to process the PiB images using Freesurfer ?


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 10 August 2017 03:41
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer PIB PET image processing

We do not have any thing to specifically analyze PiB. You can look at the 
PETsurfer page for more general instructions


On 08/09/2017 02:15 AM, M Janani wrote:
>
> Hi Team,
>
> I apologize, I am new to Freesurfer.
>
> Currently we are processing PIB PET images.
>
> When we compare the SPM data along with FREESURFER 
> outputs. We were able to see a large variation in the values.
>
> Could you please guide us in processing PIB PET images 
> in Freesurfer?
>
> Since the signal of a PET image is very weak, we used 
> MRI image as a guide to map it to Standard brain.
>
> How does Freesurfer process in this case?
>
> Your help would be grateful.
>
> Regards,
>
> Janani
>
>
>
> ::DISCLAIMER::
> 
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

[Z Hessam]

it shows:

-rwxrwxrwx 1 8481 1590 0 Aug  9 22:30
/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz


On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang 
wrote:

> Hmm, if you run:
>
> ls -l /media/hessam91/driver2/freesurfer/freesurfer/
> subjects/bert/mri/T1.mgz
>
> what does it show?
>
> On Aug 9, 2017, at 4:47 PM, Z Hessam  wrote:
>
> of course:
>
> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v
> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz
> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red
> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
>
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
> -1): read error
> MRIread failed: Unable to read from /media/hessam91/driver2/
> freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
> -1): read error
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
> -1): read error
> MRIread failed: Unable to read from /media/hessam91/driver2/
> freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
> -1): read error
>
> thanks a lot for your attention
>
> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang 
> wrote:
>
>> Can you copy and paste the exact command line you ran and the error
>> message?
>>
>> Ruopeng
>>
>>
>> On 08/09/2017 02:21 PM, Z Hessam wrote:
>>
>>
>> I try it without \ chars, works for some other subjects
>> but it doesn't work for one of them,and now I can even open it with GUI,
>> while I could open it before.
>> It seems that is time variant!
>> Should I run "recon-all ..." again for that subject?
>>
>>
>>
>>
>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl > > wrote:
>>
>>> can you try it without all the \ characters?  You shouldn't need them if
>>> it's all on one line
>>>
>>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>>
>>>
 $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
 bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
 mri_read(): couldn't determine type of file
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/
 MRIread failed: Unable to read from
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/
 mri_read(): couldn't determine type of file
 /media/hessam91/driver2/freesurfer/freesurfer/subjects/


 I use the example 4 in the "download and install" page of site

 On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <
 fis...@nmr.mgh.harvard.edu>
 wrote:

   hmmm, that looks ok, but it's hard to tell with all the
   backslashes and blank lines and such. Can you send the full
   command on a single line (e.g. by hitting up-arrow in the
   terminal window) and the actual output of freeview?

On Wed, 9 Aug 2017, Z Hessam wrote:


 Hello Freesurfer Developers,

 I have problem when I use "freeview" example code in
 terminal,
 freeview -v \

 bert/mri/T1.mgz \

 bert/mri/wm.mgz \

 bert/mri/brainmask.mgz \


 bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

 -f \

 bert/surf/lh.white:edgecolor=blue \

 bert/surf/lh.pial:edgecolor=red \

 bert/surf/rh.white:edgecolor=blue \

 bert/surf/rh.pial:edgecolor=red
 it tell "Failed to load MRI ",
 mri_read(): couldn't determine type of file
 
 MRIread failed: Unable to read from 
 mri_read(): couldn't determine type of file
 
 but i can load wm.mgz and other existed files in
 GUI.

 please help me to know why this error happend? and
 what should I do to solve
  this?

 I've searched the list, I found a similar errors,
 but wasn't helpful answer reported.
 help me please

 regards

 On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
  wrote:

 Hello Freesurfer Developers,

 I have problem when I use "freeview" example code in
 terminal,
 freeview
 -v \

 bert/mri/T1.mgz \

 bert/mri/wm.mgz \

 bert/mri/brainmask.mgz \


 bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

 -f \

 bert/surf/lh.white:edgecolor=blue \

[Freesurfer] PET surfer

[John Anderson]

Hi Dr Greve,

I have PET data for two groups and I used PET surfer in FSV 6.0 to run the 
analyses. The pipeline is straightforward and the analysis ran smoothly without 
any issues.

Is it correct procedure to adjust PET signal to differences in gray matter 
volume or cortical thinness between two groups?

In other words, is it correct if gray matter volume or cortical thickness for 
subjects be included as EVs in GLM or a nausiance factor in QDEC?

Specifically, is the PET signal changeable depending on  differences in 
cortical thickness.
or differences in gray matter volume?

Thank you  for any clarification

> Thank you !
> Jon___
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