Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 07 Mar '17

07 Mar '17

Dear Martin, I think yes, you can use PALM with FreeSurfer surfaces, see my conversation with Anderson on FSL list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL&D=0&1=FSL&9=A&… but beware not to forget to include average the vertex area (?h.white.avg.area.mgh) file. Antonin If you don't have an orthogonal design, then you can't use mri_glmfit-sim. I think you can use PALM:https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM I have not tried it yet. Anderson, can you use PALM with surfaces? On 03/06/2017 05:23 PM, Martin Juneja wrote: > Hi Dr. Greve, > > I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 > It gives error that ERROR: design matrix is not orthogonal, cannot be > used with permutation. > > But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it works. > > I am not sure whether I will have to make the design matrix > orthogonal. If so, could you please tell me how that can be done? > > Or using --perm-force should be fine? > > Thanks. > > On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve > <gr...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > This is a problem with using LGI in that it is already extremely > smooth > that the smoothness exceeds the limit of the look up table that we > supply. I recommend that you not use a gaussian-based correction for > LGI. Instead, use permutation (see mri_glmfit-sim --help). > > > > On 03/06/2017 01:36 PM, Martin Juneja wrote: > > Hello everyone, > > > > I am trying to extract clusters showing significant correlation > > between LGI and a behavioral measure. I am able to extract PCC and > > sig.mgh but at the last step when I try to run simulation command to > > view corrected results and I run: > > > > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 > > --2spaces > > > > I get following error: > > > > ERROR: cannot find > > > > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > > > > But I can see mc-z.csd file in fwhm30 etc. > > > > Full message on terminal window is attached following. > > > > Any help would be really appreciated. > > > > ----- Full message ---- > > > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd > dods --C > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir > lh.MEQ_LGI.glmdir > > > > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin > > > > SURFACE: fsaverage lh > > > > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log > > > > /usr/local/freesurfer/bin/mri_glmfit-sim > > > > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces > > > > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $ > > > > Mon Mar 6 11:11:13 MST 2017 > > > > setenv SUBJECTS_DIR > > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll > > > > FREESURFER_HOME /usr/local/freesurfer > > > > Original mri_glmfit command line: > > > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd > dods --C > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir > lh.MEQ_LGI.glmdir > > > > DoSim = 0 > > > > UseCache = 1 > > > > DoPoll = 0 > > > > DoPBSubmit = 0 > > > > DoBackground = 0 > > > > DiagCluster = 0 > > > > gd2mtx = dods > > > > fwhm = 35.073391 > > > > ERROR: cannot find > > > > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > > > >

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Re: [Freesurfer] wm.mgz manual editing, revisited
by Antonin Skoch 07 Mar '17

07 Mar '17

Dear Eli, did you read my response to your previous thread? I recommended you to try adding control points to the white matter. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51959.html Regards, Antonin Hello all, Again, I tried to modify the white matter surface by adding voxels to the wm.mgz file, and performed the reconstruction by doing the following.-Opened brainmask.mgz for reference -Opened wm.mgz on top of that -Click the voxel edit button -Check the recon editing checkbox -Fill in voxels where I want to extend the whitematter surface -Save wm.mgz -At terminal, from the appropriate subject directory, run: recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd` Once this is finished, I examine the surfaces, but they have not changed. lh/rh.white should be changed to include the voxels I painted in, correct? I have no problem removing voxels from the pial surface, but extending the white matter is for some reason not working for me, so I am really stumped as to why these wm.mgz edits aren't making any difference. Any help with this is vastly appreciated. I have tried this several times on different subjects with no luck. Here are links to some relevant files. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks, Eli

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Problem with T1 Nifti file read
by Dhaval Shah 07 Mar '17

07 Mar '17

Hi all, i am having problem with recon-all function. Whenever i call that function from a terminal with my high resolution Nifti file ("MPRAGE.nii") it aborts with an error: "nifti1Read(): unsupported slice Timing pattern in ..."path to file". Can some one please help? I need to generate Labels from this NIFTI file -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203dshah@bnac.net//http://mbl.bnac.net

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wm.mgz manual editing, revisited
by Rockers, Elijah D. 07 Mar '17

07 Mar '17

Hello all, Again, I tried to modify the white matter surface by adding voxels to the wm.mgz file, and performed the reconstruction by doing the following. -Opened brainmask.mgz for reference -Opened wm.mgz on top of that -Click the voxel edit button -Check the recon editing checkbox -Fill in voxels where I want to extend the whitematter surface -Save wm.mgz -At terminal, from the appropriate subject directory, run: recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd` Once this is finished, I examine the surfaces, but they have not changed. lh/rh.white should be changed to include the voxels I painted in, correct? I have no problem removing voxels from the pial surface, but extending the white matter is for some reason not working for me, so I am really stumped as to why these wm.mgz edits aren't making any difference. Any help with this is vastly appreciated. I have tried this several times on different subjects with no luck. Here are links to some relevant files. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Strange wm error
by Melanie Ganz 07 Mar '17

07 Mar '17

Dear list, we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine. Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views. Cheers, Mel -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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mri_segstats
by Chih-Yang Hsu 07 Mar '17

07 Mar '17

Hi, I am using Freesurfer to estimate cortical thickness. Is there any way to get all the details of the thickness distribution? I used mri_segstats but it only provided mean and standard deviation. Thank you.

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Question on saving interim files when generating an fsavearge
by West, John D. 07 Mar '17

07 Mar '17

Hello. We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us? Thanks for your help. John D. West, M.S. Principal Systems Analyst | Center for Neuroimaging Indiana University School of Medicine 355 West 16th Street | GH 4100 Indianapolis, IN 46202 317-963-7510 jdwest(a)iupui.edu<mailto:jdwest@iupui.edu>

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Re: [Freesurfer] Creating custom aparc.a2009s+aseg.mgz: Shuffled names of parcellations after mris_label2annot
by Antonin Skoch 06 Mar '17

06 Mar '17

Dear Doug, I am sorry, the problem with missing perirhinal label in .annot was due to typo in my .ctab file (also seen in my previous mail). Now it works OK. I have already solved my problem by creating annotation just of entorhinal and perirhinal labels (like I wrote in my post here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51979.html ), running it through mri_aparc2aseg and then fusing with default aparc.a2009s+aseg.mgz. It works correctly I think. Btw, just for the record, only now I have noticed that some labels in aparc.a2009s.annot in fsaverage have different names than in aparc.a2009s.annot of subject processed by recon-all. For example, anterior insula is read G_and_S_cingul-Ant in fsaverage, whereas in subject run through recon-all it reads G&S_cingul-Ant. This was another reason of missing labels in my testing .annot in fsaverage since due to the fact that .ctab file in fsaverage is not available, I used .ctab file from some of my subjects. Antonin I cannot replicate the missing last label. Can you upload the relevant data so I can take a look? Using the --l instead should work too. For your other problem, I would probably run mri_label2label with the --outstat option to create an overlay of the statistic, then create a segmentation based on the maximum stat using somethign likemri_concat label1stat.mgh ... labelNstat.mgh --max-index --o labelseg.mgh You can convert this back to labels with mri_cor2label --surf fsaverage lh --i labelseg.mgh --id 1 --l newlabel1.label On 03/02/2017 12:05 PM, Antonin Skoch wrote: > Dear Doug, > > I am using quite recent dev version built 8/2/2017. > > mris_label2annot of this version is following: > > $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve > > Regards, > > Antonin > > > what version are you using? I thought I fixed the missing-last-label > problem in v6 > On 03/01/2017 06:42 PM, Antonin Skoch wrote: > > Dear Doug, > > > > thank you, adding --no-unknown indeed fixed the global shuffling of > > the label names. However, last line of .ctab seems not to be read this > > time and produced .annot does not contain perirhinal label. > > > > My modified .ctab file looks like this: > > > > 0 Unknown 0 0 0 0 > > 1 G&S_frontomargin 23 220 60 0 > > 2 G&S_occipital_inf 23 60 180 0 > > 3 G&S_paracentral 63 100 60 0 > > 4 G&S_subcentral 63 20 220 0 > > 5 G&S_transv_frontopol 13 0 250 0 > > 6 G&S_cingul-Ant 26 60 0 0 > > 7 G&S_cingul-Mid-Ant 26 60 75 0 > > 8 G&S_cingul-Mid-Post 26 60 150 0 > > 9 G_cingul-Post-dorsal 25 60 250 0 > > 10 G_cingul-Post-ventral 60 25 25 0 > > 11 G_cuneus 180 20 20 0 > > 12 G_front_inf-Opercular 220 20 100 0 > > 13 G_front_inf-Orbital 140 60 60 0 > > 14 G_front_inf-Triangul 180 220 140 0 > > 15 G_front_middle 140 100 180 0 > > 16 G_front_sup 180 20 140 0 > > 17 G_Ins_lg&S_cent_ins 23 10 10 0 > > 18 G_insular_short 225 140 140 0 > > 19 G_occipital_middle 180 60 180 0 > > 20 G_occipital_sup 20 220 60 0 > > 21 G_oc-temp_lat-fusifor 60 20 140 0 > > 22 G_oc-temp_med-Lingual 220 180 140 0 > > 23 G_oc-temp_med-Parahip 65 100 20 0 > > 24 G_orbital 220 60 20 0 > > 25 G_pariet_inf-Angular 20 60 220 0 > > 26 G_pariet_inf-Supramar 100 100 60 0 > > 27 G_parietal_sup 220 180 220 0 > > 28 G_postcentral 20 180 140 0 > > 29 G_precentral 60 140 180 0 > > 30 G_precuneus 25 20 140 0 > > 31 G_rectus 20 60 100 0 > > 32 G_subcallosal 60 220 20 0 > > 33 G_temp_sup-G_T_transv 60 60 220 0 > > 34 G_temp_sup-Lateral 220 60 220 0 > > 35 G_temp_sup-Plan_polar 65 220 60 0 > > 36 G_temp_sup-Plan_tempo 25 140 20 0 > > 37 G_temporal_inf 220 220 100 0 > > 38 G_temporal_middle 180 60 60 0 > > 39 Lat_Fis-ant-Horizont 61 20 220 0 > > 40 Lat_Fis-ant-Vertical 61 20 60 0 > > 41 Lat_Fis-post 61 60 100 0 > > 42 Medial_wall 25 25 25 0 > > 43 Pole_occipital 140 20 60 0 > > 44 Pole_temporal 220 180 20 0 > > 45 S_calcarine 63 180 180 0 > > 46 S_central 221 20 10 0 > > 47 S_cingul-Marginalis 221 20 100 0 > > 48 S_circular_insula_ant 221 60 140 0 > > 49 S_circular_insula_inf 221 20 220 0 > > 50 S_circular_insula_sup 61 220 220 0 > > 51 S_collat_transv_ant 100 200 200 0 > > 52 S_collat_transv_post 10 200 200 0 > > 53 S_front_inf 221 220 20 0 > > 54 S_front_middle 141 20 100 0 > > 55 S_front_sup 61 220 100 0 > > 56 S_interm_prim-Jensen 141 60 20 0 > > 57 S_intrapariet&P_trans 143 20 220 0 > > 58 S_oc_middle&Lunatus 101 60 220 0 > > 59 S_oc_sup&transversal 21 20 140 0 > > 60 S_occipital_ant 61 20 180 0 > > 61 S_oc-temp_lat 221 140 20 0 > > 62 S_oc-temp_med&Lingual 141 100 220 0 > > 63 S_orbital_lateral 221 100 20 0 > > 64 S_orbital_med-olfact 181 200 20 0 > > 65 S_orbital-H_Shaped 101 20 20 0 > > 66 S_parieto_occipital 101 100 180 0 > > 67 S_pericallosal 181 220 20 0 > > 68 S_postcentral 21 140 200 0 > > 69 S_precentral-inf-part 21 20 240 0 > > 70 S_precentral-sup-part 21 20 200 0 > > 71 S_suborbital 21 20 60 0 > > 72 S_subparietal 101 60 60 0 > > 73 S_temporal_inf 21 180 180 0 > > 74 S_temporal_sup 223 220 60 0 > > 75 S_temporal_transverse 221 60 60 0 > > 76 entorhinal_exvivo.thresh 222 62 67 0 > > 77 perirhninal_exvivo.thresh 223 65 60 0 > > > > with newline in the end. > > > > However, I was able to successfully generate annotation with 2 labels > > ( previous swap of names in .annot produced using --l options was my > > fault since I did not read the help to the detail to learn that the > > order of label files of --l arguments has to match the order of names > > in .ctab). So I could possibly achieve my goal by run mri_aparc2aseg > > on this simple 2-label annot and somehow merge the result with the > > default aparc.a2009s to bring the rhinal labels into that. Do you see > > any pitfall with that? > > > > In any case, however, before running aparc2aseg I have to cope with > > another problem with rhinal labels - the rhinal.thresh labels are > > overlapping and I would need to correctly assign vertices in the label > > intersection (see my previous post > >http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51919.html > > ). > > > > Regards, > > > > Antonin > > > > > > Try adding --no-unknown to the label2annot command line > > On 02/28/2017 04:45 PM, Antonin Skoch wrote: > > > Dear experts, > > > > > > I would like to create modified aparc.a2009s+aseg file with relevant > > > parts of parahippocampal cortical ribbon voxel labels replaced by > > > labels derived from surface labels of entorhinal and parahippocampal > > > cortex (created also by default in recon-all). This modified > > > aparc.a2009s+aseg file I want to use for streamline assignment in > > > structural connectome generation in MrTrix3. > > > > > > I think that mri_label2vol is not optimal way to do it since it would > > > leave some voxels in the ribbon unassigned. > > > > > > I think that the better, but much complicated, way to do this is to > > > modify aparc.a2009s.annot with the information from these labels and > > > then run again mris_aparc2aseg. > > > > > > I tried to do this by using: > > > > > > mri_annotation2label > > > > > > and > > > > > > mris_label2annot --hemi lh --subject my_subject --ldir my_labels --a > > > my_aparc.a2009s --ctab my_aparc.annot.a2009s.ctab --debug > > > > > > I took the aparc.annot.a2009s.ctab from the my_subject/label > > > directory and added to the end 2 row with entorrhinal and perirhinal > > > parcellations with unique RGB values to assure the relevant parts of > > > parahippocampal gyrus label are replaced by these new labels I want to > > > supply. > > > > > > But the resulting new .annot file is not correct - the labels are in > > > correct position on cortical surfaces, but the label names of all > > > labels are shuffled. > > > > > > I even tried the sequence of mri_annotation2label, mris_label2annot > > > without adding new labels, just converting annotation to labels and > > > back, and the annotation naming is also corrupted. > > > > > > I also tried to create new annotation just from 2 new labels, > > > preparing .ctab file and running mris_label2annot by explicitly > > > specifying my 2 labels like > > > > > > mris_label2annot --hemi lh --subject my_subject --l > > > lh_labels/lh.perirhinal_exvivo.thresh.label --l > > > lh_labels/lh.entorhinal_exvivo.thresh.label --a rhinal_aparc.a2009s > > > --debug --ctab rhinal_aparc.annot.a2009s.ctab > > > > > > In this case the label names in annotation are swapped (entorhinal is > > > perirhinal and vice versa), swapped are also file names of labels > > > which I tried to back convert by using mri_annotation2label. > > > > > > I am using quite recent build of dev version of Freesurfer from > > > 28/2/2017. > > > > > > Could you suggest where could be the problem? > > > > > > Or could you advice different, possibly more simple way, how to > > > achieve my goal? > > > > > > Thank you in advance. > > > > > > Regards, > > > > > > Antonin Skoch

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GLM set up and correlations
by Martin Juneja 06 Mar '17

06 Mar '17

Hello experts, I am trying to correlate cortical surface area measure with behavioral measures using instructions from here: https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/GroupAnalysis After I overlay pcc.mgh (partial correlations) and sig.mgh files on lh.inflated, I see some clusters with high PCC values (Destrieux atlas) (please see attached figure) at "unlabeled subcortical regions" for one of the behavioral measures, out of 4. Although for volume and thickness versus any behavioral measures, I do not see any "unlabeled subcortical regions" clusters like this. Could you please advise me if its normal to get these clusters? If so, how can I interpret that? Or Am I doing something wrong during preprocessing? If so, any help to find out where I might be doing wrong and to fix the issue would be really appreciated. Thanks.

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Error viewing corrected results
by Martin Juneja 06 Mar '17

06 Mar '17

Hello everyone, I am trying to extract clusters showing significant correlation between LGI and a behavioral measure. I am able to extract PCC and sig.mgh but at the last step when I try to run simulation command to view corrected results and I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces I get following error: ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd But I can see mc-z.csd file in fwhm30 etc. Full message on terminal window is attached following. Any help would be really appreciated. ----- Full message ---- cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin SURFACE: fsaverage lh log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $ Mon Mar 6 11:11:13 MST 2017 setenv SUBJECTS_DIR /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 35.073391 ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd

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Freesurfer March 2017