That mris_preroc commad is incomplete.
On 8/7/19 11:13 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
My command lines:
My command lines sequentially for the analysis are: ( I have done just the same command lines for MWF maps and it worked very good, but for NDI and ODI maps of NODDI does not work).
1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
And the output for the mri_glmfit was:
ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
Reza
On 7 Aug 2019, at 17:11, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
no idea until you tell me what you did, including command lines and terminal output
On 8/7/19 11:08 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Thanks, I saw that before, what could be the reason for that and how could i do mris_preproc correctly for NDI maps?
Thanks, Reza
On 7 Aug 2019, at 17:05, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Every vertex of every subject is 0 in lh.NDI_inflated.avg.05.mgh
On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Hi Doug,
When i click on the link you sent me for uploading the files, there is no bottom/way to upload something there. That is why i attached the outputs.
My command lines sequentially for the analysis are: ( I have done just the same command lines for MWF maps and it worked very good, but for NDI and ODI maps of NODDI does not work).
1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).
2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir
The outputs of all three steps are attached.
Looking forward for your helps
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Monday, August 5, 2019 5:55:18 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Can you upload the input (ie, argument to --y) here: ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Also, send your mri_glmfit command line.
On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
yes, I have the page below for all patients.
I think it means all values are zero. My registration for bbregister is fine and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Friday, August 2, 2019 3:35:45 PM *To:* Reza Rahmanzadeh; Freesurfer support list *Cc:* greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help 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. <DGREVE@mgh.harvard.edu > mailto:DGREVE@mgh.harvard.edu> > *Sent:* Wednesday, July 31, 2019 12:50:45 AM > *To:* Reza Rahmanzadeh; Freesurfer support list > *Cc:* greve@nmr.mgh.harvard.edu mailto:greve@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:* greve@nmr.mgh.harvard.edu mailto: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: >> >> *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-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:* Tuesday, July 30, 2019 2:44:25 PM >> *To:* Greve, Douglas N.,Ph.D. >> *Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu >> mailto: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 mailto: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 >>>> 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 >>>>>> 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:* 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 >>>>>> 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_fre... > >>>>>> 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 >>>>>> 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 >>>>>> 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_fre... >>>>>> >>>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>>> 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 >>>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>>>> 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 >>>>>> 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 >>>>>>>> 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 >>>>>> 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 >>>>>>>> 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 >>>>>> 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 >>>>>> 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 > 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 >>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>> 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 >>>>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>>>>>>>>>> mailto: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 > 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 >>>>>>>> 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 >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer