Doug, did you receive my files? I received an email explaining that the mail is too big and I need to wait for an authorisation from the moderator.
Thank you, Redwan On Aug 4, 2017 10:34 AM, "Redwan Maatoug" <redwanmaat...@gmail.com> wrote: > Thank you very much Doug, I really appreciate your help and your patience, > > General purpose : in total I have 112.*nii* that I tried to convert them > to 112.*mgh* files and then to combined them in a *.annot* file with > different colors. > > FIRST ISSUE : > When I have converted the files from volumetric to surface, I have used > this command line : > *mri_vol2surf --mov parcel_1.nii **--reg MNI152_T1_brain.dat --hemi lh > --o **parcel_1.mgh* > > So this command line worked for 60 files on 112 files but for some of them > (for example *parcel_1.nii*) after the conversion the .MGH file seems to > be empty. > > Because when I use the command line mri_surfcluster to extract the > coordinates of the vertices : > (*mri_surfcluster --in parcel_1.mgh --hemi lh --subject fsaverage --thmin > 0 --nofixmni --olab parcel_1.mgh*) the label file is empty. > > when I want to display the .MGH file with the following command line I do > not see anything : > *tksurfer fsaverage lh inflated -overlay parcel_1.mgh **-fminmax .5 1 * > > BUT when i display the .NIFTI file like that : > *tkmeditfv fsaverage orig.mgz -overlay parcel_1.nii **-surfs -fminmax .5 > 1* > I see something > > First could you tell me why for some files I can convert them from .NII to > .MGH but not for all of them. > > SECOND ISSUE : > For the files, I have successfully converted (because with mri_surfcluster > I have vertices coordinates in the label files : like parcel_97.mgh and > parcel_100.mgh), could you please tell the steps to follow to display a > combined .annot file on tksurfer. > > Please find attached : > -parcel_1.nii (issue to convert from .nii to .mgh) > -parcel_1.mgh (I have the feeling that it is empty) > -brain template in MNI 152 space I have used for mri_vol2surf > -parcel_97.mgh and parcel_100.mgh (i can't display them as a combined > .annot file in tksufer) > -the ctab with all the colors for the different parcels. > > Thank you very very much, > Redwan > > On Fri, Aug 4, 2017 at 9:52 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> Yes, send me two label files and the ctab again. >> >> On 8/4/17 12:49 PM, Redwan Maatoug wrote: >> >> Hi Douglas, >> >> I tried to rename the parcel files and in the ctab but it does not change >> anything. I have the feeling that sometime label2abnot can read the colors >> because as you can see in the screenshots there is some colors on the >> brain. >> If I give you the files could you help me to follow the rights steps to >> make? Maybe I am missing something but I really need this to be done to >> compare the résultats in fMRI and in EEG. >> >> Thank you very much, >> Redwan >> >> On Aug 3, 2017 15:40, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> wrote: >> >>> that would mean that mris_label2annot is probably not reading any of >>> your labels because it is expecting the label name to be, eg, >>> lh.parcel_1.mgh-0001.label.label based on what you have told me. Try >>> changing he label name in the folder to lh.parcel_1.mgh-001.label and >>> change the ctab names to parcel_1.mgh-0001 >>> >>> >>> On 08/03/2017 06:35 PM, Redwan Maatoug wrote: >>> > In the Yeo_split_surf/ the label have exactly the same names as in the >>> > ctab. >>> > >>> > They are named like that : >>> > parcel_1.mgh-0001.label >>> > parcel_2.mgh-0001.label >>> > parcel_3.mgh-0001.label >>> > ... >>> > parcel_112.mgh-0001.label >>> > >>> > Yes we had to split the Yeo_split_surface because the goal was to do >>> > some analyzes in fMRI and EEG using the same atlas. We had to split >>> > the atlas when for example the ROI was crossing the medial line etc... >>> > >>> > But now I just want to combine the files again so it is not supposed >>> > to have overlapping no ? >>> > >>> > Thank you, >>> > Redwan >>> > >>> > On Thu, Aug 3, 2017 at 3:21 PM, Douglas N Greve >>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> > >>> > It may have to do with the label names that get created from the >>> ctab. >>> > What are the names of the labels in Yeo_split_surf/ ? I can't >>> > figure out >>> > what you are doing with that code. Looks like you have broken the >>> yeo >>> > atlas into labels, then you're combining them together again? >>> > >>> > >>> > On 08/03/2017 05:57 PM, Redwan Maatoug wrote: >>> > > Thank you ffor your quick answer, >>> > > >>> > > I have attached the --ctab >>> > > >>> > > Here is the link for the .mgh files. >>> > > >>> > > https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE >>> > <https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE> >>> > > >>> > > >>> > > So my command line to extract the coordinates from the .mgh >>> files : >>> > > >>> > > *I)* >>> > > for f in ${1}/*.mgh >>> > > do >>> > > mri_surfcluster --in ${f} --hemi lh --subject fsaverage >>> > --thmin 0 >>> > > --nofixmni --olab ./${f} >>> > > done >>> > > >>> > > _#OUTPUT for 1 file #_ >>> > > Reading source surface >>> > > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white >>> > > Done reading source surface >>> > > Computing metric properties >>> > > Loading source values >>> > > number of voxels in search space = 163842 >>> > > Done loading source values (nvtxs = 163842) >>> > > overall max = 1 at vertex 0 >>> > > overall min = 0 at vertex 1 >>> > > surface nvertices 163842 >>> > > metric props tot surface area 65416.984375 >>> > > group_avg_vtxarea_loaded 1 >>> > > masked surface area 82219.390625 >>> > > NOT Adjusting threshold for 1-tailed test >>> > > thminadj = 1 >>> > > Searching for Clusters ... >>> > > thmin=1.000000 (1.000000), thmax=-1.000000 (-1), thsignid=0, >>> > > minarea=5.000000 >>> > > Found 3 clusters >>> > > Max cluster size 4759.318359 >>> > > thsign = abs, id = 0 >>> > > version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 >>> > zkaufman >>> > > Exp $ >>> > > hemi = lh >>> > > srcid = Yeo_Split_surf/parcel_9.mgh >>> > > srcsubjid = fsaverage >>> > > srcsurf = white >>> > > srcframe = 0 >>> > > thsign = abs >>> > > thmin = 1 >>> > > thmax = -1 >>> > > fdr = -1 >>> > > minarea = 5 >>> > > xfmfile = talairach.xfm >>> > > nth = -1 >>> > > subjectsdir = /usr/local/freesurfer/subjects >>> > > FixMNI = 0 >>> > > ------------- XFM matrix (RAS2RAS) --------------- >>> > > >>> > /usr/local/freesurfer/subjects/fsaverage/mri/transforms/tal >>> airach.xfm >>> > > 1.00000 0.00000 0.00000 0.00000; >>> > > 0.00000 1.00000 0.00000 0.00000; >>> > > 0.00000 0.00000 1.00000 0.00000; >>> > > 0.00000 0.00000 0.00000 1.00000; >>> > > ---------------------------------------------------- >>> > > Reading source surface >>> > > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white >>> > > Done reading source surface >>> > > Computing metric properties >>> > > Loading source values >>> > > number of voxels in search space = 163842 >>> > > Done loading source values (nvtxs = 163842) >>> > > overall max = 1 at vertex 4422 >>> > > overall min = 0 at vertex 0 >>> > > surface nvertices 163842 >>> > > metric props tot surface area 65416.984375 >>> > > group_avg_vtxarea_loaded 1 >>> > > masked surface area 82219.390625 >>> > > NOT Adjusting threshold for 1-tailed test >>> > > thminadj = 1 >>> > > Searching for Clusters ... >>> > > thmin=1.000000 (1.000000), thmax=-1.000000 (-1), thsignid=0, >>> > > minarea=5.000000 >>> > > Found 1 clusters >>> > > Max cluster size 16.666323 >>> > > >>> > > *II)* >>> > > >>> > > mris_label2annot --s fsaverage --h lh --a combined --ctab >>> color.txt >>> > > --ldir Yeo_split_surf/ >>> > > >>> > > I tried without any improvement to add this arguments : >>> --noverbose >>> > > --thresh 1 --maxstatwinner >>> > > >>> > > >>> > > Reading ctab color.txt >>> > > >>> > > Number of ctab entries 113 >>> > > >>> > > INFO: no labels specified, generating from ctab >>> > > >>> > > _# OUTPUT #_ >>> > > >>> > > $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ >>> > > >>> > > cwd /usr/local/freesurfer/subjects >>> > > >>> > > cmdline mris_label2annot --s fsaverage --h lh --a combined --ctab >>> > > color.txt --ldir Yeo_split_surf/ >>> > > >>> > > sysname Linux >>> > > >>> > > hostname redwanmaatoug-MacBookPro >>> > > >>> > > machine x86_64 >>> > > >>> > > user redwanmaatoug >>> > > >>> > > >>> > > subject fsaverage >>> > > >>> > > hemi lh >>> > > >>> > > SUBJECTS_DIR /usr/local/freesurfer/subjects >>> > > >>> > > ColorTable color.txt >>> > > >>> > > AnnotName combined >>> > > >>> > > nlables 0 >>> > > >>> > > LabelThresh 0 0.000000 >>> > > >>> > > Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.orig >>> > > >>> > > Mapping unhit to unknown >>> > > >>> > > Found 163842 unhit vertices >>> > > >>> > > Writing annot to >>> > > /usr/local/freesurfer/subjects/fsaverage/label/lh.combined.annot >>> > > >>> > > >>> > > *III)* >>> > > >>> > > tksurfer fsaverage lh inflated -annotation >>> > > /usr/local/freesurfer/subjects/fsaverage/label/lh.combined.annot >>> > > >>> > > # OUTPUT # >>> > > >>> > > subject is fsaverage >>> > > >>> > > hemi is lh >>> > > >>> > > surface is inflated >>> > > >>> > > surfer: current subjects dir: /usr/local/freesurfer/subjects >>> > > >>> > > surfer: not in "scripts" dir ==> using cwd for session root >>> > > >>> > > surfer: session root data dir ($session) set to: >>> > > >>> > > surfer: /usr/local/freesurfer/subjects >>> > > >>> > > checking for nofix files in 'inflated' >>> > > >>> > > Reading image info (/usr/local/freesurfer/subjects/fsaverage) >>> > > >>> > > Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz >>> > > >>> > > surfer: Reading header info from >>> > > /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz >>> > > >>> > > surfer: vertices=163842, faces=327680 >>> > > >>> > > reading colortable from annotation file... >>> > > >>> > > colortable with 113 entries read (originally none) >>> > > >>> > > Found embedded color table in annotation. >>> > > >>> > > surfer: single buffered window >>> > > >>> > > surfer: tkoInitWindow(fsaverage) >>> > > >>> > > setting percentile thresholds (-1.00, 0.00, 0.00) >>> > > >>> > > surfer: using interface /usr/local/freesurfer/tktools/ >>> tksurfer.tcl >>> > > >>> > > Reading /usr/local/freesurfer/tktools/tkm_common.tcl >>> > > >>> > > Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl >>> > > >>> > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl >>> > > >>> > > Reading /usr/local/freesurfer/tktools/tkUtils.tcl >>> > > >>> > > Successfully parsed tksurfer.tcl >>> > > >>> > > reading white matter vertex locations... >>> > > >>> > > >>> > > >>> > > Thank you very much, >>> > > >>> > > >>> > > Redwan >>> > > >>> > > On Thu, Aug 3, 2017 at 1:30 PM, Redwan Maatoug >>> > > <redwanmaat...@gmail.com <mailto:redwanmaat...@gmail.com> >>> > <mailto:redwanmaat...@gmail.com <mailto:redwanmaat...@gmail.com>>> >>> > wrote: >>> > > >>> > > Hi all, >>> > > >>> > > So my issue is the following : >>> > > >>> > > I have 112 mgh files. (They come from the Yeo 17 Network >>> > atlas (we >>> > > split the atlas in smaller regions). I have extracted the >>> > > coordinates with : >>> > > mri_surfcluster (playing with the thmin option) >>> > > mri_vol2label >>> > > >>> > > and then I have used mri_label2annot with my own color lookup >>> > > table to combine the 112 files into 1 file. (I have played >>> with >>> > > --noverbose, --maxstatwinner) >>> > > >>> > > When I try to display, I have the feeling that there is some >>> > > overlapping because what tksufer dispays, is not very >>> > relevant and >>> > > it is spotty. >>> > > >>> > > I have attached some screenshots >>> > > Thank you very much for your help, >>> > > Redwan >>> > > >>> > > >>> > > >>> > > >>> > > _______________________________________________ >>> > > Freesurfer mailing list >>> > > Freesurfer@nmr.mgh.harvard.edu >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > >>> > -- >>> > Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> > Phone Number: 617-724-2358 <tel:617-724-2358> >>> > Fax: 617-726-7422 <tel:617-726-7422> >>> > >>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> > <https://gate.nmr.mgh.harvard.edu/filedrop2> >>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > Outgoing: >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har >>> vard.edu> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > >>> > >>> > 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 >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >
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