Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Thalamic segmentation
by 郑凤莲 18 Apr '19

18 Apr '19

External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by /opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the latest version of Freeview. However, I can't find this version on Freesurferwiki. Could you share me the install steps and the latest version? Thanks very much for your help. Sincerely, Zheng

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same aparc ROI with mri_label2vol?
by Sam W. 17 Apr '19

17 Apr '19

External Email - Use Caution Hi, I created a series of labels with mri_annotation2label (aparc.a2009s labels) and then created a reg file with: tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg register.dat and the volume: mri_label2vol --label labels/lh.G_cingul-Post-dorsal.label --temp mri/rawavg.mgz --subject bert --hemi lh --o roi-in-rawavg.nii.gz --proj frac 0 1 .1 --fillthresh .3 --reg register.dat When I load the roi-in-rawavg.nii.gz and the aparc.a2009+aseg.mgz volume in freeview there are parts of the Cingulum in the aparc.a2009+aseg that are not included in the roi-in-rawavg. Probably this is related to the -fillthresh and -proj thresholds. Is there a way to get exactly the same ROI with mri_label2vol as shown in the aparc.a2008+aseg volume? Best regards, Sam

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same output with vol2vol and label2vol
by Sam W. 17 Apr '19

17 Apr '19

External Email - Use Caution Hi, In a Freesurfer help webpage it says that to convert an image (eg brain.mgz) from freesurfer to anatomical native space (eg rawavg.mgz) we should use mri_vol2vol, but for a segmentation (aseg.mgz) we should use mri_label2vol. I converted the aseg.mgz of bert using both vol2vol and label2vol and found no difference - The resulting output images look exactly the same. Is there really an advantage of using label2vol instead of vol2vol? Thanks! Sam

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correlation analysis
by TMS lab 17 Apr '19

17 Apr '19

External Email - Use Caution mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. < DGREVE(a)mgh.harvard.edu> ha scritto: > what is your command line? > > On 4/11/19 3:53 PM, TMS lab wrote: > > > > External Email - Use Caution > > > > Unfortunately I get such error message with the matrix 0 0 0 1 > > ERROR: dimension mismatch between X and contrast contrast.mtx X has > > 3 cols, C has 4 cols > > > > Instead if I use 0 0 1, it works > > > > Best, > > RAFAEL > > That should have failed because it only has 3 values (should have 4). I > > think it should be 0 0 0 1 > > > > > > On 4/11/19 3:20 AM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > You are right. I want simply to correlate myelin and nhpt regressing > > > out age. > > > I did it with the following matrix: > > > 0 0 1 > > > And it seems to work. Is it ok this matrix? > > > > > > Thanks a lot > > > Rafael > > > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > > <DGREVE(a)mgh.harvard.edu > > <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu > > <mailto:DGREVE@mgh.harvard.edu>>> ha scritto: > > > > > > That will compute the average of the Age slope and the NHPT slope. > > > Probably not what you want to do > > > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Dear Freesurfer team, > > > > > > > > I'm running a correlation analysis where I'd like to corelate > > > > myelination and a clinical parameter (NHPT) regressing out the > > > effect > > > > of age. > > > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > > > This is my FSGD FILE: > > > > GroupDescriptorFile 1 > > > > Title Myelin > > > > Class Main > > > > Variables Age NHPT > > > > Inputfs_CGaMain 19 18.2 > > > > ....... > > > > > > > > Is the matrix ok? > > > > > > > > Thanks > > > > Rafael > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > RispondiRispondi a tuttiInoltra > > > > > > > > > > > > > > Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna(a)gmail.com > > <mailto:tmslabna@gmail.com>> ha scritto: > > > > You are right. I want simply to correlate myelin and nhpt > > regressing out age. > > I did it with the following matrix: > > 0 0 1 > > And it seems to work. Is it ok this matrix? > > > > Thanks a lot > > Rafael > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha scritto: > > > > That will compute the average of the Age slope and the NHPT > > slope. > > Probably not what you want to do > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > Dear Freesurfer team, > > > > > > I'm running a correlation analysis where I'd like to corelate > > > myelination and a clinical parameter (NHPT) regressing out > > the effect > > > of age. > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > This is my FSGD FILE: > > > GroupDescriptorFile 1 > > > Title Myelin > > > Class Main > > > Variables Age NHPT > > > Inputfs_CGaMain 19 18.2 > > > ....... > > > > > > Is the matrix ok? > > > > > > Thanks > > > Rafael > > > > > > _______________________________________________ > > > 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 > > 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] 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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