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. > <dgr...@mgh.harvard.edu <mailto:dgr...@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. >>>> <dgr...@mgh.harvard.edu <mailto:dgr...@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. <dgr...@mgh.harvard.edu >>>>> <mailto:dgr...@mgh.harvard.edu>> >>>>> *Sent:* Monday, August 5, 2019 5:55:18 PM >>>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>>> *Cc:* gr...@nmr.mgh.harvard.edu <mailto:gr...@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. <dgr...@mgh.harvard.edu >>>>>> <mailto:dgr...@mgh.harvard.edu>> >>>>>> *Sent:* Friday, August 2, 2019 3:35:45 PM >>>>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>>>> *Cc:* gr...@nmr.mgh.harvard.edu <mailto:gr...@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. <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 >>>>>>> <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 >>
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