did you check each subject to make sure they had a non-zero map?
On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
NODDI is diffusion imaging and we have vakue regarding neurite density (NDI in
NDI map) and orientation dispersion (ODI value in ODI map). I do not know why
mris_preproc works well on MWI maps but not on NODDI maps (both NDI and ODI
maps). Beside using projfrac-avg 0 1 0.25 , i have run mris_preproc with
projfrac 0.5 but again i got this error:
ERROR: no voxels found in the mask
make sure at least one voxel has a non-zero value for each input
I have run mris_preproc on three patients that i am sure about registration
quality, again when i scroll through them , there is no value in none of them.
How that is possible?
NODDI does not have a lot of zero value but all values in cortex are between
0.2-0.4.
Thanks,
Reza
________________________________
From: Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, July 31, 2019 12:50:45 AM
To: Reza Rahmanzadeh; Freesurfer support list
Cc: gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] need for help
I don't know what is in the NODDI maps. The way mri_glmfit works is that
if any subject has a 0-value at a vertex, then it will mask out that
vertex for all subjects. Is NODDI something that might have a lot of
0-values? It also may be that one subject has all 0s (eg, if the
regitration was really bad), so you can check the map created by
mris_preproc (load it in as an overlay, then hit the configure button,
then change the frame number to scroll through your subjects)
On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:
>
> 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:* gr...@nmr.mgh.harvard.edu<mailto:gr...@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:
>
> *F**ound 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> on behalf of Reza Rahmanzadeh
> <reza.rahmanza...@unibas.ch><mailto:reza.rahmanza...@unibas.ch>
> *Sent:* Tuesday, July 30, 2019 2:44:25 PM
> *To:* Greve, Douglas N.,Ph.D.
> *Cc:* Freesurfer support list;
> gr...@nmr.mgh.harvard.edu<mailto:gr...@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.
> <dgr...@mgh.harvard.edu><mailto:dgr...@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.
> >> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >> <mailto:dgr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Reza
> >>>> Rahmanzadeh
> >>>> <reza.rahmanza...@unibas.ch<mailto:reza.rahmanza...@unibas.ch>
> >>>> <mailto:reza.rahmanza...@unibas.ch>>
> >>>> *Sent:* Monday, July 29, 2019 11:37:46 AM
> >>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list;
> >>>> gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
> >>>> <mailto:gr...@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.
> >>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@mgh.harvard.edu>>
> >>>> *Sent:* Wednesday, July 17, 2019 5:31:27 PM
> >>>> *To:* Reza Rahmanzadeh; Freesurfer support list;
> >>>> gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
> >>>> <mailto:gr...@nmr.mgh.harvard.edu>
> >>>> <mailto:gr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Reza
> >>>> Rahmanzadeh
> >>>>> <reza.rahmanza...@unibas.ch<mailto:reza.rahmanza...@unibas.ch>
> >>>>> <mailto:reza.rahmanza...@unibas.ch>
> >>>>> <mailto:reza.rahmanza...@unibas.ch>>
> >>>>> *Sent:* Wednesday, July 17, 2019 4:26:21 PM
> >>>>> *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list;
> >>>>> gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
> >>>>> <mailto:gr...@nmr.mgh.harvard.edu>
> >>>>> <mailto:gr...@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.
> >>>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>> <mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@mgh.harvard.edu>>
> >>>>> *Sent:* Wednesday, July 17, 2019 4:14:41 PM
> >>>>> *To:* Reza Rahmanzadeh; Freesurfer support list;
> >>>> gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
> >>>> <mailto:gr...@nmr.mgh.harvard.edu>
> >>>> <mailto:gr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Reza
> >>>>>> Rahmanzadeh
> >>>>>> <reza.rahmanza...@unibas.ch<mailto:reza.rahmanza...@unibas.ch>
> >>>>>> <mailto:reza.rahmanza...@unibas.ch>
> >>>> <mailto:reza.rahmanza...@unibas.ch>>
> >>>>>> *Sent:* Wednesday, July 17, 2019 9:56:00 AM
> >>>>>> *To:* Freesurfer support list
> >>>>>> *Cc:* dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>>> <mailto:dgr...@mgh.harvard.edu>
> >>>>>> <mailto:dgr...@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...@rcmd.org<mailto:ts...@rcmd.org>
> >>>>>>> <mailto:ts...@rcmd.org>
> >>>> <mailto:ts...@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.rahmanza...@unibas.ch<mailto:reza.rahmanza...@unibas.ch>
> >>>>>> <mailto:reza.rahmanza...@unibas.ch>
> >>>>>> <mailto:reza.rahmanza...@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.
> >>>>>>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>>>>> <mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@mgh.harvard.edu>>
> >>>>>>>> Sent: Tuesday, July 16, 2019 10:01:15 PM
> >>>>>>>> To: Reza Rahmanzadeh; Freesurfer support list;
> >>>>>> gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
> >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
> >>>>>> <mailto:gr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>>>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Greve,
> >>>> Douglas
> >>>>>>>>> N.,Ph.D. <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>>>>>> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@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>
> >>>> <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.
> >>>>>>>>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>>>>>>> <mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@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>
> >>>> <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.
> >>>>>>>>>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>>>>>>>> <mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@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.
> >>>>>>>>>>>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> >>>>>>>>>>>> <mailto:dgr...@mgh.harvard.edu>
> >>>> <mailto:dgr...@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>
> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>>>>>>>>>>> *Cc:* gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
> >>>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
> >>>> <mailto:gr...@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>
> >>>> <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>
> >>>> <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>
> >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Freesurfer mailing list
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> >>>>>> <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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