External Email - Use Caution        

(sorry for bombaeding you with e-mails)


It seems that the error happens only when i use NODDI diffusion image e.g. NDI map i get that error, but for MWIs the new mris_preproc works well.


Should i do anything special for NODDI images? BTW, the bbregister works well for NODDI and i entered the correct registration file into mris_preproc.


Thanks,

Reza

From: Reza Rahmanzadeh
Sent: Tuesday, July 30, 2019 6:17:22 PM
To: Greve, Douglas N.,Ph.D.; Freesurfer support list
Cc: greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for help
 

... One problem when i use the new mris_preproc:

Always the output of mri_glmfit when the input is the result of new mris_preproc is:

Found 0 voxels in mask
ERROR: no voxels found in the mask
  make sure at least one voxel has a non-zero value for each input


I think it means that something is perhaps wrong with the script. I tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same error.  I did not get the error when i used old mris_preproc using projfrac 0.5.

The other thing that could be the reason is my fsgd file. I have problem how to specify the name of subjects,
Now it is sth like:


GroupDescriptorFile 1
Class Group1
CLASS Group2
Input FSC001 Group1
Input FSC002 Group1
Input FSC003 Group1
.

.

.

Input FSP001 Group2
Input FSP002 Group2
Input FSP003 Group2
.

.


The oeder is thew same with mris_preproc, now the subject name is FSC0xx for controls and FSP00x for patients, these are the name of folders containing FS outputs, but my input volume is MWIs and the registration files are not stored in this folder. Does it matter how to name subjects when i am using fsgd file only in mri_glmfit ( to get aware of order)?


Thanks,

Reza




From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch>
Sent: Tuesday, July 30, 2019 2:44:25 PM
To: Greve, Douglas N.,Ph.D.
Cc: Freesurfer support list; greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for help
 
        External Email - Use Caution       

Thanks Doug,

The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?


Thanks,
Reza

> On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
>
> Oh, I guess that's a problem! I've created a new version here
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
> See if that works. You should compare the output to using the max or
> -projfrac 0.5 to make sure they are at least similar since I have not
> run it even once:)
>
>
>> On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
>>
>>         External Email - Use Caution
>>
>> Thanks
>>
>> But mris_prepoc will not accept “projfrac-avg” and there’s an error:
>> argument unrecognized!
>>
>> Then how can i compute the average via mris_preproc? As based on
>> tutorial, first i used tkregister/bbregister to compute the
>> registration matrix and then i should put input images with
>> transformation matrix in mris_preproc. I mean i shouldn’t use
>> mri_vol2surf (that allows me to use projfrac-avg) in group analysis
>> and that’s the reason i have problem with mris_proproc to compute the
>> average.
>>
>> What should i do?
>>
>> Thanks,
>> Reza
>>
>> On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D.
>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>>
>>> one computes the average, the other computes the maximum
>>>
>>>> On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Dear Doug,
>>>>
>>>>
>>>> I appreciat if you reply my question in the previous e-mail with this:
>>>>
>>>>
>>>> can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max
>>>> delta just the same?
>>>>
>>>>
>>>> Best,
>>>>
>>>> Reza
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <freesurfer-bounces@nmr.mgh.harvard.edu
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Reza
>>>> Rahmanzadeh
>>>> <reza.rahmanzadeh@unibas.ch <mailto:reza.rahmanzadeh@unibas.ch>>
>>>> *Sent:* Monday, July 29, 2019 11:37:46 AM
>>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list;
>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>> *Subject:* Re: [Freesurfer] need for help
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Dear Doug,
>>>>
>>>>
>>>> Thanks, the tutorial was super helpful. As i would compare the MWF
>>>> value in cortex between control subjects and patients. Now my problem
>>>> is how to make the contrast matrix for mris_preproc to do the
>>>> comparison in both direction (in 1, the outcome should be voxels in
>>>> which MWf value in control>patients & in 2, reversed).
>>>>
>>>>
>>>> The explanations in
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
>>>>
>>>> is for one group analysis and in
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is
>>>> not clear about contrast.
>>>>
>>>> I remember for -randomise command-line, there was possibility to make
>>>> contrast and design matrix (something like FSGD) via design_ttest2.
>>>> Can i use still design_ttest2 for producing contrast and design matrix?
>>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>> Reza
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>> <mailto:DGREVE@mgh.harvard.edu>>
>>>> *Sent:* Wednesday, July 17, 2019 5:31:27 PM
>>>> *To:* Reza Rahmanzadeh; Freesurfer support list;
>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>> *Subject:* Re: [Freesurfer] need for help
>>>> Ah, I see. Try this tutorial. It is for fMRI, but it applies to any
>>>> modality
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
>>>>
>>>>
>>>>> On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
>>>>>
>>>>>         External Email - Use Caution
>>>>>
>>>>> to clarify better, i need to compare myelin water fraction in cortex
>>>>> of control and patients to find out the areas with reduced MWF in
>>>>> patients cortex compared with controls, that is the reason i want to
>>>>> have cortex in inflated format.
>>>>>
>>>>>
>>>>> For this reason i used bbregister to have register.dat, and then
>>>>> mri_vol2surf to resample MWI cortex to surface. As i need to have all
>>>>> surfaces in fsaverage space for group analysis, i am using
>>>>> mri_preproc7mri_surf2surf (according to the group analysis wiki you
>>>>> sent me).
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu
>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Reza
>>>> Rahmanzadeh
>>>>> <reza.rahmanzadeh@unibas.ch <mailto:reza.rahmanzadeh@unibas.ch>
>>>>> <mailto:reza.rahmanzadeh@unibas.ch>>
>>>>> *Sent:* Wednesday, July 17, 2019 4:26:21 PM
>>>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list;
>>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>>> *Subject:* Re: [Freesurfer] need for help
>>>>>
>>>>>         External Email - Use Caution
>>>>>
>>>>> I am trying to compare MWI(sampled on the  surface) between couple
>>>>> patients and controls using group analysis, therefore i need to have
>>>>> all inflated surface_on_same space (according to the wiki of group
>>>>> analysis you sent me, i should use mris_preproc to put my data on
>>>>> fsaverage).
>>>>>
>>>>>
>>>>> Could you now tell me whether my mris_prepoc is right? and one other
>>>>> question i have asked in last email?
>>>>>
>>>>>
>>>>> Thanks a lot,
>>>>>
>>>>> Reza
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>> <mailto:DGREVE@mgh.harvard.edu>>
>>>>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM
>>>>> *To:* Reza Rahmanzadeh; Freesurfer support list;
>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>>> *Subject:* Re: [Freesurfer] need for help
>>>>> It is not clear to me what you are trying to do. Do you want to do a
>>>>> morphometry study (ie, comparing thickness, area, and/or volume across
>>>>> subjects)? Or do you want to compare MWI (sampled on the  surface)
>>>>> across subjects?
>>>>>
>>>>>> On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>>
>>>>>> Dear Doug,
>>>>>>
>>>>>>
>>>>>> I took the back slash away and ran
>>>>>>
>>>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out
>>>>>> lh.FSP10.white.mgh --meas white
>>>>>>
>>>>>>
>>>>>> but i got error:
>>>>>>
>>>>>> *Reading curvature file
>>>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white**
>>>>>> MRISreadBinaryCurvature: incompatible vertex number in file
>>>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white**
>>>>>> ERROR: reading curvature file*
>>>>>>
>>>>>>
>>>>>> Then i changed it to --meas : mris_preproc --target fsaverage --hemi
>>>>>> lh --s FSP010 --out lh.FSP10.white.mgz --meas area
>>>>>>
>>>>>>
>>>>>> Then, as i need to register my the inflated cortex of myelin water
>>>>>> image (MWI) to the surface_registered_on_fsaverage (could it be the
>>>>>> output of command-line above?), should i use this output
>>>>>> "lh.FSP10.white.mgz" and the output of mri_vol2surf (resampling
>>>>>> myelin water image to lh.white of my subject FSP10 before
>>>>>> registration to fsaverage) for mri_surf2surf (to resample the latter
>>>>>> to the former, to have MWI to surface_fsaverage)
>>>>>>
>>>>>>
>>>>>>
>>>>>> Looking forward to answers
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Reza
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>> ------------------------------------------------------------------------
>>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Reza
>>>>>> Rahmanzadeh <reza.rahmanzadeh@unibas.ch
>>>>>> <mailto:reza.rahmanzadeh@unibas.ch>
>>>> <mailto:reza.rahmanzadeh@unibas.ch>>
>>>>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM
>>>>>> *To:* Freesurfer support list
>>>>>> *Cc:* DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
>>>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>>>> *Subject:* Re: [Freesurfer] need for help
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Thanks Tim,
>>>>>>
>>>>>> Then if i would resample my data to fsaverage and surfaces are of
>>>>>> main importance to my work, what should i use for -meas ?
>>>>>>
>>>>>> Reza
>>>>>>
>>>>>>> On 17 Jul 2019, at 09:39, Tim Schäfer <ts+ml@rcmd.org
>>>>>>> <mailto:ts+ml@rcmd.org>
>>>> <mailto:ts+ml@rcmd.org>> wrote:
>>>>>>>
>>>>>>>         External Email - Use Caution
>>>>>>>
>>>>>>> I guess '-meas' expects a measure (like 'thickness' or 'area'), not
>>>>>> a surface (like 'white').
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Tim
>>>>>>>
>>>>>>>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
>>>>>> <reza.rahmanzadeh@unibas.ch <mailto:reza.rahmanzadeh@unibas.ch>
>>>>>> <mailto:reza.rahmanzadeh@unibas.ch>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>         External Email - Use Caution
>>>>>>>>
>>>>>>>> I removed the back slash and the command line i executed is:
>>>>>>>>
>>>>>>>>
>>>>>>>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out
>>>>>> lh.FSP10.white.mgh --meas white
>>>>>>>>
>>>>>>>>
>>>>>>>> but i got the error:
>>>>>>>>
>>>>>>>> Reading curvature file
>>>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white
>>>>>>>> MRISreadBinaryCurvature: incompatible vertex number in file
>>>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white
>>>>>>>> ERROR: reading curvature file
>>>>>>>>
>>>>>>>> I have added --srcfmt mgh as the last argument, but again i got
>>>>>> the error:
>>>>>>>> Reading source surface reg
>>>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
>>>>>>>> Loading source data
>>>>>>>> No such file or directory
>>>>>>>> ERROR: could not read
>>>>>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white as type 3
>>>>>>>>
>>>>>>>>
>>>>>>>> What is wrong with my mris_prepoc command line?
>>>>>>>>
>>>>>>>> Reza
>>>>>>>>
>>>>>>>>
>>>>>>>> ________________________________
>>>>>>>> From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>> <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM
>>>>>>>> To: Reza Rahmanzadeh; Freesurfer support list;
>>>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>>>>>> Subject: Re: need for help
>>>>>>>>
>>>>>>>> don't include the back slash (ie, fsaverage not fsaverage/ same
>>>>>> for FSP010)
>>>>>>>>
>>>>>>>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
>>>>>>>>>
>>>>>>>>>         External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Thanks a lot Doug,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I started to proceed with FS group analysis wiki you sent to me.
>>>>>>>>> Accordingly, i have to resample all my data (output of recon-all
>>>>>> for a
>>>>>>>>> given subject for example) into fsaverage using mris_preproc. My
>>>>>>>>> commandline for a subject was:
>>>>>>>>>
>>>>>>>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out
>>>>>>>>> lh.FSP10.white.mgh --meas white
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> and i got the error:
>>>>>>>>>
>>>>>>>>> *
>>>>>>>>> *
>>>>>>>>> *Reading source surface reg
>>>>>>>>>
>>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>>>> No such file or directory
>>>>>>>>> mri_surf2surf: could not read surface
>>>>>>>>>
>>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>>>>>>>> No such file or directory*
>>>>>>>>> *
>>>>>>>>> *
>>>>>>>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one
>>>> file
>>>>>>>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder
>>>>>>>>> with the name lh.fsaverage and i copied/pasted the mentiomed file
>>>>>> into
>>>>>>>>> this folder and i changed the file name to: ./sphere.reg. I got the
>>>>>>>>> error:
>>>>>>>>> *
>>>>>>>>> *
>>>>>>>>> *Reading curvature file
>>>>>>>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere
>>>>>>>>> MRISreadBinaryCurvature: incompatible vertex number in file
>>>>>>>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
>>>>>>>>> *
>>>>>>>>> *
>>>>>>>>> *
>>>>>>>>> *
>>>>>>>>> What is the problem with my mris_preproc command-line?
>>>>>>>>>
>>>>>>>>> Reza
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>> ------------------------------------------------------------------------
>>>>>>>>> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Greve,
>>>> Douglas
>>>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM
>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> *Subject:* Re: [Freesurfer] need for help
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
>>>>>>>>>>
>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> (I assume now we are discussing in FS list, if no please let
>>>> me how
>>>>>>>>>> possible?)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks Doug, now i could see the inflate surface, this means
>>>> that my
>>>>>>>>>> mri_vol2surf works well. As i would do GLM analysis over inflated
>>>>>>>>>> cortex of patients and controls in Qdec,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 1- should i input my surfaces to Qdec as inflated surface or just
>>>>>>>>>> inputting the output_of_vol2surf.mgz to Qdec?
>>>>>>>>>>
>>>>>>>>>> if inflated one is the input, then how could i get them?
>>>>>> mris_inflate
>>>>>>>>>> gives error.
>>>>>>>>>>
>>>>>>>>> QDEC is no longer being supported. Use the command line stream
>>>>>>>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim).
>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 2- should i input all patients and controls surfaces in standard
>>>>>>>>>> surface before entering to Qdec?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 3- I would like to resample whole cortex (whole cortical
>>>>>> thickness, in
>>>>>>>>>> other words: the average of all projfrac between 0 and 1), is it
>>>>>>>>>> possible? or i am limited to resample one given depth of
>>>> cortex into
>>>>>>>>>> inflated surface only?
>>>>>>>>>>
>>>>>>>>> Run mri_vol2surf with --help and look for --projfrac-avg
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> thanks a lot,
>>>>>>>>>>
>>>>>>>>>> Reza
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>
>>>> ------------------------------------------------------------------------
>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>> <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM
>>>>>>>>>> *To:* Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu
>>>>>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> *Subject:* Re: need for help
>>>>>>>>>> The command should be something like
>>>>>>>>>> tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz
>>>>>>>>>> Also, tksurfer is also obsolete (but should work). You should be
>>>>>> using
>>>>>>>>>> freeview (or tksurferfv, a freeview front end that takes the same
>>>>>>>>>> command line args as tksurfer)
>>>>>>>>>> Also, please remember to respond to the fs list
>>>>>>>>>>
>>>>>>>>>>> On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
>>>>>>>>>>>
>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>> I got the mri_vol2surf output with .mgz:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> my tksurfer command:
>>>>>>>>>>>
>>>>>>>>>>> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of
>>>>>>>>>>> mri_vol2surf was lh.inflated_MWI.mgz)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> and the error i got:
>>>>>>>>>>>
>>>>>>>>>>> *freadFloat: fread failed**
>>>>>>>>>>> No such file or directory*
>>>>>>>>>>>
>>>>>>>>>>> To me, opening the surfer in tksurfer is only a way to get
>>>> sure my
>>>>>>>>>>> vol2surf worked well. the main problem is i got this error
>>>> for all
>>>>>>>>>>> mris_smooth, mris_inflate, mris_sphere ...
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Do you think that means the output of mri_vol2surf is not
>>>>>> correct, or
>>>>>>>>>>> otherwise i could proceed with that , even when tksurfer
>>>> could not
>>>>>>>>>>> open it, for GLM in Qdec?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Reza
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>> ------------------------------------------------------------------------
>>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>> <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 6:01:15 PM
>>>>>>>>>>> *To:* Reza Rahmanzadeh
>>>>>>>>>>> *Subject:* Re: need for help
>>>>>>>>>>> what is your tksurfer command line? Also, the .w file is somewhat
>>>>>>>>>>> obsolete (it should still work); instead you can use .mgz
>>>> file (and
>>>>>>>>>>> don't spec --paint)
>>>>>>>>>>>
>>>>>>>>>>>> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks Doug,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I used the one without --inflated also, again the tksurfer
>>>>>> could not
>>>>>>>>>>>> open it and i got the same error. Where is the problem with my
>>>>>> cmd.?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> In addition, i wanted to make the output of mri_vol2surf
>>>> inflated
>>>>>>>>>>>> using mris_inflate but i got the same error:
>>>>>>>>>>>>
>>>>>>>>>>>> *freadFloat: fread failed
>>>>>>>>>>>> No such file or directory*
>>>>>>>>>>>> *
>>>>>>>>>>>> *
>>>>>>>>>>>> *could you let me know what is the problem in registering my mwi
>>>>>>>>>>>> volumes to surface that i getonly such errors.*
>>>>>>>>>>>> *
>>>>>>>>>>>> *
>>>>>>>>>>>> *Thanks,*
>>>>>>>>>>>> *reza
>>>>>>>>>>>> *
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>
>>>> ------------------------------------------------------------------------
>>>>>>>>>>>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>
>>>> <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM
>>>>>>>>>>>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu
>>>>>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>> <mailto:greve@nmr.mgh.harvard.edu>
>>>>>>>>>>>> *Subject:* Re: need for help
>>>>>>>>>>>> Don't use --inflated. The inflated surface is not a biological
>>>>>>>>>>>> surface. The default is the white surface, which is the one
>>>>>> you want
>>>>>>>>>>>> (--projfrac 0.5 will project it to the middle between the
>>>>>> white and
>>>>>>>>>> pial)
>>>>>>>>>>>>
>>>>>>>>>>>>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> External Email - Use Caution
>>>>>>>>>>>>>
>>>>>>>>>>>>> Dear Freesurfer,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I have a batch of myelin water image (MWI) from patients and
>>>>>>>>>>>>> controls, and trying to have inflated cortex registered on
>>>>>> standard
>>>>>>>>>>>>> surface for GLM (Qdec).
>>>>>>>>>>>>>
>>>>>>>>>>>>> With the commandlines below i get my inflated surface of MWI
>>>>>> map of
>>>>>>>>>>>>> my patients and controls.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1-using bbregister to put MWI into FS space and to calculate
>>>>>>>>>>>>> register.dat:
>>>>>>>>>>>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg
>>>>>> register.dat
>>>>>>>>>>>>> --o mwf_FS --t1
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2-using mri_vol2surf to extract inflated surface of MWI:
>>>>>>>>>>>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5
>>>>>>>>>>>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type
>>>>>>>>>>>>> paint--inflated (*or*--surf sphere)
>>>>>>>>>>>>>
>>>>>>>>>>>>> However the tksurfer could not open the inflated surface
>>>> and the
>>>>>>>>>>>>> error message is:
>>>>>>>>>>>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices!
>>>>>>>>>>>>> Probably trying to use a scalar data file as a surface!*
>>>>>>>>>>>>>
>>>>>>>>>>>>> I used the commandline below for #2:
>>>>>>>>>>>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o
>>>>>>>>>>>>> mwf-lh.w --out_type paint
>>>>>>>>>>>>> and i got the error:
>>>>>>>>>>>>>
>>>>>>>>>>>>> *ERROR: MRISread: file
>>>>>>>>>>>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has
>>>>>> many
>>>>>>>>>>>>> more faces than vertices!**
>>>>>>>>>>>>> Probably trying to use a scalar data file as a surface!*
>>>>>>>>>>>>> *
>>>>>>>>>>>>> *
>>>>>>>>>>>>> As tksurfer could not open my surfaces with errors above, i
>>>> think
>>>>>>>>>>>>> perhaps the vol2surf procedure is not done properly. Where
>>>> is the
>>>>>>>>>>>>> problem? i need to get the inflated cortex and then putting ob
>>>>>>>>>>>>> sphere (using mris_sphere) and the registering to standard
>>>>>> surface
>>>>>>>>>>>>> using mris_register for GLM in Qdec, right?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> It is two weeks i am struggling with these commands, any helps
>>>>>>>>>>>>> highly appreciated. *
>>>>>>>>>>>>> *
>>>>>>>>>>>>> *
>>>>>>>>>>>>> *
>>>>>>>>>>>>> *
>>>>>>>>>>>>> *
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> Reza
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 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.
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>> --
>>>>>>> Dr. Tim Schäfer
>>>>>>> Postdoc Computational Neuroimaging
>>>>>>> Department of Child and Adolescent Psychiatry, Psychosomatics and
>>>>>> Psychotherapy
>>>>>>> University Hospital Frankfurt, Goethe University Frankfurt am Main,
>>>>>> Germany
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>
>>>
>

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