Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

apart.a2009s naming convention: from "_and_" to "&"
by Jyrki Ahveninen 17 Aug '19

17 Aug '19

Hi guys, I (and probably others) have noticed the aparc.a2009s label naming convention has changed in recons starting from 6.0. “_and_” has become “&”, such as in lh.G&S_subcentral. It is fixable, but it may become a bit confusing for those who use fsaverage vs. individually segmented labels in a study that uses the different versions of 6.0 and beyond (e.g., those interested in using the subpmillmeter recon option). And & is also a special character, too. It is completely fixable, of course, but I just thought to bring this up, because it might cause confusion in some users. (For me, it was just a “why the xxxx does not my mris_divide_parcellation splittable” moment.) Thankfully, Jyrki

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FreeSurfer 6 vertex-wise cortical volume computation details?
by Tim Schäfer 17 Aug '19

17 Aug '19

External Email - Use Caution Dear FreeSurfer experts, can anybody refer me to a publication that explains in detail how vertex-wise cortical volume (the data in <subject>/surf/?h.volume) is computed in FreeSurfer 6? My understanding is the following: * area is computed as 1/3 the area of all triangles meeting at that vertex. * thickness is the shortest distance from the vertex (at white surface) to any vertex on pial, then the other way around from that pial vertex, divided by two. * volume is area * thickness Is that true, and where can I read up on it? Thanks, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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spatial scale bar question
by Nasiriavanaki, Zahra 16 Aug '19

16 Aug '19

Dear Freesurfers Hi I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain. I couldn't find a scale bar option in Freeview neither. I appreciate if you could let me know how to get a scale bar. Thanks Mona

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Conversions between MNI152, MNI305 & surface
by Lauri Tuominen 15 Aug '19

15 Aug '19

External Email - Use Caution Hello! I keep having 2 somewhat related problems: 1. How to convert a single coordinate from MNI305 to surface. Previosly Doug suggested to try the example 8b in https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. However, that one is about moving a coordinate from 152 to 305. I would like to know how to show that MNI305 coordinate on a surface so I could eyeball it with tksurfer. Maybe one of the examples on that page is the one I am looking for but I don’t understand which one it could be. 2. How to transform a volume between MNI152 & MNI305 spaces. I tried: a) mri_vol2vol --targ ${my_volume_in_MNI305} --inv --mov $FSL_DIR/data/standard/MNI152lin_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o I_hope_this_volume_is_in_MNI152 b) mri_vol2vol --mov ${my_volume_in_MNI305} --MNI152reg --o I_really_hope_this_volume_is_in_MNI152 Neither of these methods seem to work. a-method moves the image too much anteriorly, and the b-method posteriorly. Thank you in advance, any help will be greatly appreciated! Thank you so much! Lauri

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mris_convert segmentation fault on R hemisphere aparc.a2009s only?
by Damion V Demeter 15 Aug '19

15 Aug '19

External Email - Use Caution I am having an issue processing some of my subjects through the HCP pipeline and have no idea what this error means. If anyone could help out, I'd appreciate it! Here is all the info: 1. Some (not all) of my subjects are getting a segmentation fault error during the post-freesurfer step of the HCP pipeline. Previous subjects were fully processed fine without error (over 100 of them) and are from the same group (all scanner and acquisition settings identical). Here is the segmentation fault error line: FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 294: 46979 Segmentation fault mris_convert --annot "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii 2. I have narrowed down this error further and have found that it only happens on the right hemisphere aparc.a2009s file. I have manually run the command above for the left and right hemisphere files separately as a test, and the L hemisphere files complete without fail. The R hemisphere, however, always gets this segmentation fault. This only occurs on certain subjects, but all the files this command is using look good and error free. All previous steps appeared to finish without fail and all expected files were written and can be opened (I'm 99% sure...I might have missed something). I am at a complete loss at how to troubleshoot this further or fix this error. Does anyone have any ideas or solutions? Thank you!

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Issues with set-up and configuration on Linux
by Collins Jones, Liam 15 Aug '19

15 Aug '19

External Email - Use Caution Dear FreeSurfer developers, I am having trouble with FreeSurfer set up and configuration on Linux. The installation appears to have completed without any problems, though when pasting the lines export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh into the terminal command window I am seeing the following:- -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni bash: tr: No such file or directory bash: grep: No such file or directory bash: tr: No such file or directory bash: sed: No such file or directory FSL_DIR /usr/share/fsl/5.0 Following this, when running the first command from the "Test your FreeSurfer installation" section of the Download website, I'm seeing this error:- Command 'cp' is available in '/bin/cp' The command could not be located because '/bin' is not included in the PATH environment variable. I am not sure why this error is occurring and have been through the archive but could not find a similar problem. In addition to this I'm unable to run basic Linux commands (eg ls) in the same terminal window. Is there a way to overcome this so that I can run FreeSurfer functions? Any help would be greatly appreciated. Here are some background details:- 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: Ubuntu 18.04.2 LTS 3) uname -a: Linux bodhi 4.15.0-55-generic #60-Ubuntu SMP Tue Jul 2 18:22:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Many thanks, Liam Collins-Jones.

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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help
by Greve, Douglas N.,Ph.D. 15 Aug '19

15 Aug '19

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(a)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(a)mgh.harvard.edu> >>> *Sent:* Monday, August 5, 2019 5:55:18 PM >>> *To:* Reza Rahmanzadeh; Freesurfer support list >>> *Cc:* greve(a)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(a)mgh.harvard.edu> >>>> *Sent:* Friday, August 2, 2019 3:35:45 PM >>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>> *Cc:* greve(a)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(a)mgh.harvard.edu> >>>>> *Sent:* Wednesday, July 31, 2019 12:50:45 AM >>>>> *To:* Reza Rahmanzadeh; Freesurfer support list >>>>> *Cc:* greve(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Reza >>>>> Rahmanzadeh >>>>>> <reza.rahmanzadeh(a)unibas.ch> >>>>>> *Sent:* Tuesday, July 30, 2019 2:44:25 PM >>>>>> *To:* Greve, Douglas N.,Ph.D. >>>>>> *Cc:* Freesurfer support list; greve(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of >>>>> Reza >>>>>>>>>> Rahmanzadeh >>>>>>>>>> <reza.rahmanzadeh(a)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(a)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_fr… >>>>> >>>>>>>>>> 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(a)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(a)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_fr… >>>>>>>>>> >>>>>>>>>>> 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(a)nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>>> <freesurfer-bounces(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>>>> <freesurfer-bounces(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>> <freesurfer-bounces(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>>>>> *Cc:* greve(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Using Freesurfer Commands for Neonate
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Lilla, Thanks for your help. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gcamri/aseg.auto_noCCseg.label_intensities.txt" which used a predefined file from freesurfer folder. Actually, I used the mri_aparc2aseg command with some changes, seen bellow: mri_aparc2aseg --s mysubj --annot aparc --o $SUBJECTS_DIR/mysubj/mri/parc.mgz so, I am wondered if it reads the ' /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I would appreciate it of you could help on how to correct this part. Regards, Mahshid

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Re: [Freesurfer] How to Divide the Brain Surface Parcells to more regions
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Doug, Special appreciation for your help. Actually, I have created the annotation and the color table files and finally I have divided the parcels. Also, I checked the primary and the division parcels on the .pial surface that they were correct. But as I bring them from surface to volume using mri_aparc2aseg (as mentioned in the email, Subject: How to Create Cortex Parcellation Using "mri_aparc2aseg"?) it fail. I mean that the parcels are not placed where they should be there. In other word, I expect it when a primary region had been divided to for example two other regions finally, the two regions with each other form the primary region with the same shape and position in the brain cortex. But, it does not happen!!! All newly resulted regions are in the brain cortex and seem well in total but they do not placed correctly based on primary regions and have movement and region shape deformation when put them beside each other to have a one region as one of the primaries. So that I doubt about the freesurfer commands that basically are used for adults, while I use neonate images. I am really confused, I would appreciate it if you could help me. Best Regards, Mahshid

1 0

Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Doug, Here is the emails: Message: 6 Date: Fri, 2 Aug 2019 01:55:34 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"? To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <183e8a60-1cc2-1680-26a7-bce8a1d03315(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" If you look in the recon-all.log file for any subject, you will see a mri_aparc2aseg command line. YOu can use that specifying your annot and the new output name. On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote: External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels: mri_aparc2aseg --s subject name --annot annotation name --o output name and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not?? Any help would be appreciated. Regards, Mahshid

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