Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file
by Mcnorgan, Christopher 17 Apr '19

17 Apr '19

External Email - Use Caution Hi Doug, After some false starts, I may have uploaded CM_f.nii.gz to the /transfer/incoming folder (my ftp client reports the upload was complete, but the directory listing afterwards shows 0 files). In the event that my ftp client lied to me about the transfer completing successfully, I have also uploaded the file to my google drive where I’ll let it remain for the next few days if you want to get it from there instead: https://drive.google.com/open?id=1urPlFg3NU56RxtZslgLzk-pXef3Csye1 Thanks, Chris From: "Mcnorgan, Christopher" <cpmcnorg(a)buffalo.edu<mailto:cpmcnorg@buffalo.edu>> Subject: [Freesurfer] Followup on the mystery of the missing mcprextreg file Date: April 16, 2019 at 5:55:28 PM EDT To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> External Email - Use Caution Hi Doug, For some reason I’m having a problem replying to this list with my reply to your reply. To recap: some of my functional runs are missing the mcprextreg file, and so the GLM with the motion correction parameters is failing. You had asked whether a mc-subjectname-bold.log file exists for these data. These log files do exist, and I’ve tried a couple times to send the log files (1MB attachment rejected). I’m including a google drive link to one of the log files in the hopes that your offer still stands to get to the bottom of why these files are reliably not being created for some runs, while created for other runs collected during the same session: https://drive.google.com/open?id=17GLikK1mzY5uL52TyqlGK0Sa5N5Fy1KY We’ve been acutely aware of how many data frames are in each 4D volume because the scanner has been incorrectly writing that all volumes are 256 frames, though our self-paced experiment terminates earlier to that. We accidentally found the fix to be to open up the header using fsledithd, which then zero-pads the missing data frames until we have 256. However this is the case for all runs, so that doesn’t explain why only some runs are failing. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file Date: April 16, 2019 at 6:03:01 PM EDT To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Can you upload the functional volume to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is

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Re: [Freesurfer] Help
by Alvarado,Luis R 17 Apr '19

17 Apr '19

External Email - Use Caution Please disregard this last email. I was trying to make adjustments to my mail list settings by following these instructions from the welcome email: You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu<mailto:Freesurfer-request@nmr.mgh.harvard.edu> with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. Luis R. Alvarado Ph.D. Candidate Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Where is the BrainVolStatsFixed patch?
by Alvarado,Luis R 17 Apr '19

17 Apr '19

External Email - Use Caution Dear Freesurfers, I just read the page about “Fixing of Morphometry Stats and Global Measure of Volume” on the freesurfer website <https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed>. I am, however, a bit confused about the location of the BrainVolStatsFixed patch. The page states “the problem has been fixed and a patch put here: (To be determined)”. Does anyone know the location of the patch? Best, Luis R. Alvarado Ph.D. Candidate Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Help
by Alvarado,Luis R 17 Apr '19

17 Apr '19

External Email - Use Caution

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mri_vol2surf error
by Loïc Daumail 17 Apr '19

17 Apr '19

External Email - Use Caution Dear Freesurfer experts, I am currently trying to use mri_vol2surf on my bold data. I typed this commandline : " mri_vol2surf --mov ${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz \ --mni152reg \ --projfrac-avg 0.2 0.8 0.1 \ --trgsubject fsaverage5 \ --interp nearest \ --hemi ${hemi} \ --surf-fwhm 6.0 --cortex --noreshape \ --o ${dir1}/${subject}/${subject}${scan}.fsa5.${hemi}.mgz " However, when trying to run it, I obtain the following error: ERROR: could not read .. as type 24 detail: " srcvol = /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage5 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 niiRead(): error opening file /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz ERROR: could not read /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz as type 24 " but when converting from nii.gz to mgz, I obtain the following : " mri_convert /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz... niiRead(): error opening file /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz srcvol = /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage5 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 mghRead(/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz, -1): could not open file ERROR: could not read /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz as type 3 " I also copied the output from mri_info on my bold image in .nii.gz format: " mri_info sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz Volume information for sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz type: nii dimensions: 91 x 109 x 91 x 200 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 182.000 dof: 0 xstart: -91.0, xend: 91.0 ystart: -109.0, yend: 109.0 zstart: -91.0, zend: 91.0 TR: 3220.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 200 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 2.0000 0.0000 0.0000 -90.5000 0.0000 2.0000 0.0000 -126.5000 0.0000 0.0000 2.0000 -72.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 8 ras to voxel transform: 0.5000 -0.0000 -0.0000 45.2500 -0.0000 0.5000 -0.0000 63.2500 -0.0000 -0.0000 0.5000 36.2500 0.0000 0.0000 0.0000 1.0000 " Thanks in advance for your help, Sincerely, Loïc Daumail Université Lyon 1

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Research fellow / postdoc position in 7T (f)MRI brainstem imaging
by Jacobs, H (NP) 17 Apr '19

17 Apr '19

External Email - Use Caution Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work on research related to multi-modal 7T (f)MRI imaging of the brainstem in aging under the mentorship of Dr. Heidi Jacobs. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including at ultra-high-field. It is also equipped with a substantial large scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Applicants must have obtained or anticipate soon receiving a Ph.D. in biomedical, computer or electrical engineering, medical physics, cognitive neuroscience or a related field. Strong analytical, quantitative and programming skills are essential (e.g., QSM, fMRI-physiological data analyses). Prior experience in medical imaging, signal/image processing, and physiological investigation is advantageous. The successful candidate will have joint appointments at MGH and HMS and will be closely interacting with the Harvard Aging Brain Study team (Drs. Keith Johnson and Reisa Sperling). If interested, please send your CV, letter describing interests, background, qualifications and 3 letters of recommendation. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. Heidi Jacobs, Ph.D. Instructor, GCMI Email: hjacobs(a)mgh.harvard.edu [cid:image001.png@01D4F544.4ACC20E0]Gordon Center for Medical Imaging MGH – Nashua 6606; Radiology, MGH 125 Nashua Street Street Boston, MA 02114 See also: https://www.massgeneral.org/careers/ [job number 3091900]

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Freeview update error
by Kelly Vaughn 17 Apr '19

17 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I am having trouble opening the updated version of Freeview. I have followed the directions for Linux on the UpdateFreeview site ( http://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview) but when I get to the last step and type freeview I get the following error: freeview: symbol lookup error: freesurfer/lib/qt/plugins/platforms/../../lib/libQt5XcbQpa.so.5: undefined symbol: FT_Get_Font_Format I have not found anyone reporting similar errors online. Does anyone have any thoughts on what this error means and what I can do to fix it? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20190416-14809f1 2) Platform: Red Hat Enterprise Linux 7 Thank you, Kelly Vaughn

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Re: [Freesurfer] regions of Yeo 17 networks in fast
by stdp82＠virgilio.it 16 Apr '19

16 Apr '19

External Email - Use Caution The problem persists. We are sure that the command lines which I'm using are corrected? mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt > Il 27 marzo 2019 alle 15.40 Aihuiping Xue <xueaihuiping(a)gmail.com> ha scritto: > > Hi Stefano, > > I created a lookup table for your case. You can load your .mgz file and try this lookup table in freeview. > > This is a temporary solution. We will modify the annot files and provide another version of lookup table. But that will take some time. I hope this lookup table can solve your problem for now. > > Best Regards, > XUE Aihuiping > > < stdp82(a)virgilio.it mailto:stdp82@virgilio.it > 于2019年3月27日周三下午10:26写道： > > > > > > Yes the left hemisphere is fine. > > > > The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt. > > > > Thanks > > > > Stefano > > > > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < ythomas(a)csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto: > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > Hi Stefano, > > > > > > Sorry. Can you confirm left hemisphere is ok? > > > > > > I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114. > > > > > > Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon. > > > > > > Regards, > > > Thomas > > > > > > On Wed, Mar 27, 2019 at 6:14 PM < stdp82(a)virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > > > I have renumbered and run: > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt > > > > When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal. > > > > > > > > What's happened? > > > > > > > > Thanks > > > > > > > > Best regards, > > > > > > > > Stefano > > > > > > > > > > > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < ythomas(a)csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto: > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > > > > > Renumber for visualization purpose. > > > > > > > > > > Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit. > > > > > > > > > > Thanks, > > > > > Thomas > > > > > > > > > > On Tue, Mar 26, 2019 at 6:44 PM < stdp82(a)virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > > > > > > > > > > > Thanks. > > > > > > > > > > > > Should I renumber for visualization purpose or for fs-fast? > > > > > > > > > > > > How can I do it? > > > > > > > > > > > > > > > > > > > > > > > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas(a)csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto: > > > > > > > > > > > > > > Hi Stefano, > > > > > > > > > > > > > > Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? > > > > > > > > > > > > > > If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. > > > > > > > > > > > > > > If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parc…) but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. > > > > > > > > > > > > > > Regards, > > > > > > > Thomas > > > > > > > > > > > > > > On Sun, Mar 24, 2019 at 12:18 AM < stdp82(a)virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi, my concern is the mri_aparc2aseg command line. > > > > > > > > > > > > > > > > In summary, I have done: > > > > > > > > > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot > > > > > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > > > > > > > > > > > > > The output is correct by the color label is those of aparc. > > > > > > > > > > > > > > > > Probably the error is the match between the annotations and annot-table. > > > > > > > > > > > > > > > > Could you check the command lines, please? > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE(a)mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto: > > > > > > > > > > > > > > > > > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. > > > > > > > > > > > > > > > > > > On 3/10/19 4:05 PM, stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > > > > > I will use freeview. > > > > > > > > > > > > > > > > > > > > Have you any suggestion on the use of fcseed-config option? > > > > > > > > > > > > > > > > > > > > Are you agree with the command line listed below? > > > > > > > > > > > > > > > > > > > > fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite > > > > > > > > > > > > > > > > > > > > My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? > > > > > > > > > > > > > > > > > > > > How can I select a specific seed (id) to be used in -segids? > > > > > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> mailto:fischl@nmr.mgh.harvard.edu ha scritto: > > > > > > > > > > > > > > > > > > > > > > Hi Stefano > > > > > > > > > > > > > > > > > > > > > > is there a reason you are using tkmedit and not freeview? We deprecated > > > > > > > > > > > tkmedit a long time ago now > > > > > > > > > > > > > > > > > > > > > > cheers > > > > > > > > > > > Bruce > > > > > > > > > > > On Sun, 10 Mar 2019, stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > > > > > > > > > Thanks. > > > > > > > > > > > > > > > > > > > > > > > > My error is in tkmedit > > > > > > > > > > > > > > > > > > > > > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > > > > > > > > > > > > > > > > > > > > > Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas(a)csail.mit.edu> mailto:ythomas@csail.mit.edu ha scritto: > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > > > > > > > > > Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? > > > > > > > > > > > > Your tkmedit command seems to assume Yeo_17Net.mgz is in > > > > > > > > > > > > /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? > > > > > > > > > > > > > > > > > > > > > > > > On Sat, Mar 9, 2019 at 5:47 PM < stdp82(a)virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > > > > > > > > > I have run: > > > > > > > > > > > > > > > > > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 > > > > > > > > > > > > 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > > > > > > > > > > > > > > > > > > > > > to check the output > > > > > > > > > > > > > > > > > > > > > > > > tksurfer subj rh inflated -annot > > > > > > > > > > > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot > > > > > > > > > > > > > > > > > > > > > > > > My concern is here: > > > > > > > > > > > > > > > > > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 > > > > > > > > > > > > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU > > > > > > > > > > > > T_freeview.txt --sval-annot > > > > > > > > > > > > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot > > > > > > > > > > > > > > > > > > > > > > > > tkmeditfv fsaverage orig.mgz -ov > > > > > > > > > > > > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz > > > > > > > > > > > > > > > > > > > > > > > > Yeo_17Net.mgz is empty. > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." > > > > > > > > > > > > <DGREVE(a)mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto: > > > > > > > > > > > > > > > > > > > > > > > > You have to convert the annotation to a volume using mri_aparc2aseg > > > > > > > > > > > > (look at recon-all.log for an example, but note that you'll need to > > > > > > > > > > > > specify the output so that it does not overwrite). You'll then need to > > > > > > > > > > > > look in the output segmentation and see what the segmentation ids are > > > > > > > > > > > > > > > > > > > > > > > > On 3/7/19 4:13 PM, stdp82(a)virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > > > > > > > > > Hi list, > > > > > > > > > > > > > > > > > > > > > > > > I'd like to use the regions included in Yeo 17 networks > > > > > > > > > > > > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… > > > > > > > > > > > > ring). > > > > > > > > > > > > > > > > > > > > > > > > in FS-FAST. > > > > > > > > > > > > > > > > > > > > > > > > Which is the command line to be used to create a segmentation in > > > > > > > > > > > > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd > > > > > > > > > > > > like > > > > > > > > > > > > to use it to run fcseed-config, specify -seg yourseg.mgz > > > > > > > > > > > > -segid). > > > > > > > > > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > > > Freesurfer(a)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 > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > > > Freesurfer(a)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 > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > > > Freesurfer(a)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 > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)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 > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > >

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Holes in labels (Brainnetome) after conversion from surface to volumetric space
by Caroline Chwiesko 16 Apr '19

16 Apr '19

External Email - Use Caution Hello Freesurfers developers, I am very new to freesurfer. After getting the brainnetome parcellations using freesurfer, we need to convert the BN_Atlas.annot file from surface space into volumetric space. But the problem we have is that the converted labels have holes inside (see attached image 1). I am aware that this problem has been mentioned on this mailing list. But the suggested solution to use mri_label2vol –seg aparc + aseg.mgz will not work for us as the Brainnetome script does not output such files. We tried two different ways (see below), which did not result in success. 1. This command successfully brings the labels from surface to volumetric space but gives us the holes inside the labels. Mri_label2vol --annot BN_Atlas.annot --subject 1000 --hemi lh --o xxxx/xxx/xxxxx/xxxxx/BN_Atlas.mgz --identity --temp xxx/xxxxxx/xxxxx/brain.mgz --proj frac 0 1 0.5 2. I emailed the Brainnetome authors and they suggested the command below. (In the command below I am trying to convert only 9 Brainnetome labels, just to see, if it will work). mri_annotation2label --subject 1001_20180507_MPRAGE --hemi lh --annotation BN_Atlas --sd /tmp/yassamri/R21/caro/Freesurfer/Freesurfer --labelbase /tmp/yassamri/R21/caro/Freesurfer/Freesurfer/1001_20180507_MPRAGE/test/lh.BN mri_label2vol --label lh.BN-000.label --label lh.BN-001.label --label lh.BN-003.label --label lh.BN-005.label --label lh.BN-007.label --label lh.BN-009.label --label lh.BN-009.label --label lh.BN-011.label --label lh.BN-013.label --subject 1001_20180507_MPRAGE --sd /tmp/yassamri/R21/caro/Freesurfer/Freesurfer/ --hemi lh --identity --fill-ribbon --o final.nii.gz This approach results in converted labels in volumetric space without holes, but all the labels have the value 1 (see attached image 2). But we need to keep the correct Brainnetome label values in volumetric space. What command/options could I use to overcome the problem with the holes and convert the file BN_Atlas.annot into volumetric space while keeping the Brainnetome label values? Thank you very much for your help in advance!! Carolin Our freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c we run it on Linux, kernel version 4.15.0-46-generic, Ubuntu 18.04.1 LTS [image: image001.png] [image: Screen Shot 2019-04-11 at 5.46.19 PM.png]

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Followup on the mystery of the missing mcprextreg file
by Mcnorgan, Christopher 16 Apr '19

16 Apr '19

External Email - Use Caution Hi Doug, For some reason I’m having a problem replying to this list with my reply to your reply. To recap: some of my functional runs are missing the mcprextreg file, and so the GLM with the motion correction parameters is failing. You had asked whether a mc-subjectname-bold.log file exists for these data. These log files do exist, and I’ve tried a couple times to send the log files (1MB attachment rejected). I’m including a google drive link to one of the log files in the hopes that your offer still stands to get to the bottom of why these files are reliably not being created for some runs, while created for other runs collected during the same session: https://drive.google.com/open?id=17GLikK1mzY5uL52TyqlGK0Sa5N5Fy1KY We’ve been acutely aware of how many data frames are in each 4D volume because the scanner has been incorrectly writing that all volumes are 256 frames, though our self-paced experiment terminates earlier to that. We accidentally found the fix to be to open up the header using fsledithd, which then zero-pads the missing data frames until we have 256. However this is the case for all runs, so that doesn’t explain why only some runs are failing. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Freesurfer April 2019