Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

'help: aparcstats2table'
by Zeynep Boz 02 Jun '21

02 Jun '21

External Email - Use Caution Hello, I am using Ubuntu 18.05 version and Freesurfer6 version. I've completed all the recon-all parts without any problems, but I'm having trouble with the "aparcstats2table" part. The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness --tablefile lh.thicknes.xlsx" gives the following error: File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas volume --stats = aseg.stats --table = segstats.txt" gives the following error: File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Thank you in advance for your support Dr.Zeynep YÜKSEL Ondokuz Mayis University Vocational School of Health Services, Medical İmaging 55139, Atakum, Samsun, Turkey Tel: +903623121919 Ext:5261

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mris_fix_topology taking ages
by Ellen Ji 02 Jun '21

02 Jun '21

External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_…, but wasn't able to load the &h.defect_labels as I received the error below. Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong? FYI, I'm running recon-all thru the HCP Pipeline. Thanks! tksurfer avoss_01 lh defect_labels subject is avoss_01 hemi is lh surface is defect_labels surfer: current subjects dir: /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf checking for nofix files in 'defect_labels' Reading image info (/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01) Reading /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz surfer: Reading header info from /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz nquads=4063237, nvertices=664 ERROR: MRISread: file '/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory

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Time courses and Yeo’s boundaries
by stdp82＠virgilio.it 02 Jun '21

02 Jun '21

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Recon-all error :Segmentation fault (core dumped)
by liub 02 Jun '21

02 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of running,there was an error: mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul Segmentation fault (core dumped) Command exited with non-zero status 1 Also when I ran the command "recon-all -all -s bert" using the official data in */freesurfer/subjects/bert ,it raised the same error. I googled this error,but there's still no answer.I've attached the recon-all.log. The recon-all.log is belong to bert and recon-all(1).log is belong to my data. Here is my operating system info : uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Platform: CentOS Linux release 8.3.2011 FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1 Thank you for your kind help. Best regards.

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Freeview mghRead error
by Duvnjak, Aleksandar 02 Jun '21

02 Jun '21

External Email - Use Caution Dear Freesurfer Developers, I have recently switched to a Mac for ease of use and have encountered an error upon trying to view output files from a previous data cohort which were processed on a remote computing server and copied to this Mac's local drive. I am able to view all surfaces and volumes of the native bert tutorial set, however am unable to view my own outputs. In the terminal I receive the following error: Katarinas-MacBook-Pro:mdc026 kduvnjak$ freeview -v /Applications/freesurfer/subjects/mdc026/mri/wm.mgz mghRead(/Applications/freesurfer/subjects/mdc026/mri/wm.mgz, -1): could not open file MRIread failed: Unable to read from /Applications/freesurfer/subjects/mdc026/mri/wm.mgz mghRead(/Applications/freesurfer/subjects/mdc026/mri/wm.mgz, -1): could not open file 2021-06-02 11:07:49.903 Freeview[6760:441577] modalSession has been exited prematurely - check for a reentrant call to endModalSession: Please find below any additional relevant information: Freesurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 (freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg<https://secure-web.cisco.com/13d8iRus52q-OHqUT-mKsxtr9lAYTVlnK-JKuHKACZf9jO…>) Platform: macOS Sierra Version 10.12.6 uname -a: Darwin Katarinas-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Dec 20 21:53:35 PST 2018; root:xnu-3789.73.31~1/RELEASE_X86_64 x86_64 I am also strangely unable to attach the recon-all file to this email. Perhaps this is some sort of permissions issue, although I have sudo chown for this user on the dir and that didn't seem to help. Kind regards, Aleksandar

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FW: [All] Postdoctoral position at the Multicultural Alzheimer's Prevention Program
by Fischl, Bruce 01 Jun '21

01 Jun '21

Contact Dr. Quiroz If you are interested in the postdoc opportunity below Bruce From: all-bounces(a)nmr.mgh.harvard.edu <all-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Quiroz, Yakeel T.,Ph.D. Sent: Tuesday, June 1, 2021 8:44 PM To: all(a)nmr.mgh.harvard.edu Subject: [All] Postdoctoral position at the Multicultural Alzheimer's Prevention Program Dear all, I hope everyone is doing well, I recently received another grant to use multimodal imaging and biomarkers to study cognitive decline in older Latinos, and I'm currently looking to recruit 1-2 postdoctoral fellows to join my group. I'd appreciate any help sharing this info with your colleagues! Any interested parties can contact me directly, Thanks in advance for the help! Yakeel T. Quiroz, PhD Associate Professor | Harvard Medical School MGH Research Scholar | Massachusetts General Hospital Departments of Psychiatry and Neurology Director, Familial Dementia Neuroimaging Lab Director, Multicultural Alzheimer's Prevention Program-MAPP Email: yquiroz(a)mgh.harvard.edu<mailto:yquiroz@mgh.harvard.edu> Phone: (617) 643-5944 @ytquiroz

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Re: [Freesurfer] Freesurfer- subcortical group analysis
by Douglas N. Greve 01 Jun '21

01 Jun '21

There are not results to visualize, there is just a table. There should be a sig table in the output folder On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote: > > External Email - Use Caution > > So so sorry to bother you again - hopefully the last time... > > I have followed your suggestion and that has worked, having used this > command > > mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd dods > \--C groupdiff.mtx \--glmdir aseg.glmdir > > I am now trying to visualise the results according to FSwiki, used > this command > > freeview -f > /usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50 > -viewport 3d > > I get the following error > > ERROR: reading /usr/local/freesurfer/subjects > Read 0 bytes, expected 1 > Read 0 bytes, expected 1 > /freesurfer/subjects > MRISread failed > > I wonder is this means there is something wrong with the GLM I created > or if it is something wrong with my Freeview? > > Thanks a lot in advance! > Kind regards, > Francisca > > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* 27 May 2021 21:05 > *To:* Aldinhas De Freitas Ferreira, Francisca > <francisca.ferreira.16(a)ucl.ac.uk> > *Subject:* Re: Freesurfer- subcortical group analysis > Hi Francisca, if you run asegstats2table on your group to create a > group table (subjects on the rows, structures on the columns, each > element being the structure volume for that subject), then you can use > mri_glmfit with the --table option (instead of --y). You may want to > correct for intracranial volume by adding --etiv to the > asegstats2table command. > doug > > > On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote: >> >> External Email - Use Caution >> >> Dear Dr Greve, >> >> My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging PhD >> student at the FIL in UCL. I have recently contacted Eugenio >> Iglesias, who kindly pointed me in your direction. Sorry to bother >> you, I have been working with Freesurfer and I was hoping you would >> kindly give me your opinion? >> >> I am looking to compare responders vs non responders to deep brain >> stimulation of a subcortical structure called ventral tegmental area. >> I ran recon-all, and thought Freesurfer could be useful for this task >> as it now has a brainstem segmenting module that I’ve installed. >> >> I thought I could use brainstem or subcortical volumes/surfaces to do >> the glm group analysis? (in my case regressing out age and gender). >> It seems that all the options i found on mri_glm only allow >> surface-based analysis? (the flags available being - - cortex or - >> -non-cortex) is there any way around this? >> >> I am sorry for any lack of background knowledge- which stems from the >> fact that I am primarily a clinician... >> I’d be most grateful for any suggestions! >> >> Kind regards, >> Francisca > > 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 Mass > General Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately. Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. >

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Re: [Freesurfer] PVC to calculate myelin maps
by Marina Fernández 01 Jun '21

01 Jun '21

External Email - Use Caution Thank you very much for your response Doug. What PVC method is most recommended to use to calculate the T1 / T2 ratio (RBV or MG)? And what value of PSF should we specify to calculate this ratio? To my knowledge, this is an acquisition related parameter and if I set it to 0 I will turn off PVC. Best wishes, Marina. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Douglas N. Greve <https://secure-web.cisco.com/1y-OD2P8BWHc0h287Xl8Diwwr6Ds9fMYa9s6RyGJbPbpYx…> Mon, 31 May 2021 17:39:23 -0700 <https://secure-web.cisco.com/1cF0PzjgERhEsaW2ZJdBauXH4XR9YM93MndhHQk1vpHHyU…> Yes, you can use PETsurfer. I would apply it to the ratio On 5/28/2021 10:25 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*. Can I use the PVC functions of PetSurfer for this purpose? And in case I can: Should I apply PVC only on T1? Or also in T2? Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)? Any other advice for calculating myelin maps would be welcome. Thank you in advance, Marina *Link: *MailScanner has detected a possible fraud attempt from " secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1QZOfvqmKfuLQOn-6qhxRHDDmKDXv8lZm-TGv73nobyUAH… < https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsO… >

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mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)
by Diógenes Bispo 01 Jun '21

01 Jun '21

External Email - Use Caution Hi Freesurfer team. I made the following command: #!/bin/tcsh setenv study $argv[1] foreach hemi (lh rh) foreach smoothing (10) foreach meas (volume) mris_preproc --fsgd FSGD/{$study}.fsgd \ --cache-in {$meas}.fwhm{$smoothing}.fsaverage \ --target fsaverage \ --hemi {$hemi} \ --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh end end end ---- #!/bin/tcsh set study = $argv[1] foreach hemi (lh rh) foreach smoothness (10) foreach meas (volume) mri_glmfit \ --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \ --fsgd FSGD/{$study}.fsgd dods \ --C Contrasts/Contrast-1_group.diff.mtx \ --C Contrasts/Contrast-2_group-x-age.mtx \ --C Contrasts/Contrast-3_group-x-icv.mtx \ --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \ --C Contrasts/Contrast-5_GCCV.intercept.mtx \ --C Contrasts/Contrast-6_GCCV.age.mtx \ --surf fsaverage {$hemi} \ --cortex \ --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \ --eres-save end end end ---- #!/bin/tcsh setenv study $argv[1] foreach meas (volume) foreach hemi (lh rh) foreach smoothness (10) foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir) mri_glmfit-sim \ --glmdir {$dir} \ --grf 2.0 neg \ --cwp 0.05 \ --2spaces \ end end end end I have the following error: ... mri_surfcluster --in rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask rh.volume.covid.10.glmdir/mask.mgh --cwsig rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh --sum rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary --ocn rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh --no-fixmni --csd-out rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd --fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg --oannot rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot --bonferroni 2 --surf white ERROR: need --csd with --csd-out How should I proceed to solve this problem? Thanks Diógenes Bispo diogenesdiego(a)gmail.com

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OHBM Brainhack 2021
by tibor.auer＠gmail.com 01 Jun '21

01 Jun '21

External Email - Use Caution Dear all, We are happy to announce the upcoming Organization for Human Brain Mapping (OHBM) Brainhack 2021 happening June 16-18 around the clock around the world! Join the party by registering here <https://secure-web.cisco.com/1u2I1GuBsfMI2DztYAaydXDkB0RNxUncy__lFbm-SDdTWm… tings&action=startRegistration&conferenceID=136&reginit=1&pageID=4073> ($25 fee, or optional fee waiver; check out some project proposals here <https://secure-web.cisco.com/1UFXLRFeTjTUKpaCUe2A5OoP6MkJNr_s4w0USA_K3ZpLEM…> ). We are also looking for volunteers to help spread the word and facilitate Brainhack activities. We'd like to recruit around 100 volunteers-so any contribution is more than welcome, no prerequisites needed! Volunteer by filling out this form <https://secure-web.cisco.com/1fj3giytjty06ouXa4eieRxeQrKqnaUTei05izNvGIf01X…> (more information about volunteer roles here <https://secure-web.cisco.com/114kTuwVJBTKR8p5Z7O5ECuQ0yNJyNNG7W9ImirtCxFrNF… 2LG8/edit> ). About Brainhack: Brainhacks <https://secure-web.cisco.com/1OFqeoe3DhJ2HFRk731XAuL_ZhIr3mkQLrs1klsF23uuCs…> (including OHBM Brainhack <https://secure-web.cisco.com/1KlYvRlwLlb7R-u7A-iVfMxqZxByTv1jlTSvCNbGksHAxN…> ) are events promoting interdisciplinary neuroscience research; they bring researchers together from a variety of subfields (e.g., neurobiology, psychology, computer science, etc.) and research backgrounds (e.g., medical student, industry professional, RA, etc.) to collaborate on projects and ideas and teach open science-oriented technical skills. The focus on intensive community- and skill-building opens doors to a number of professional opportunities (learn more about these benefits here <https://secure-web.cisco.com/1ek4KT5yiBQGfsE5TvK-ZoFBZ7UwbmOkcRm2cDDK0U-v5B…> ). Brainhacks are not your typical hackathon-they are actively inclusive rather than competitive. To that end, even if you have never attended a hackathon before or written a line of code, you are welcome! No need to work with neuroimaging methods or be part of OHBM to attend. All you need is to come along and share your ideas, expertise, contributions with whatever pace and form you can make it happen while having a chance to collaborate and meet with many other researchers all around the world! We particularly welcome the contributions of groups traditionally underrepresented in neuroscience, including women, BIPOC, LGBTQ+, individuals with disabilities, and more. Brainhacks are safe spaces, with a policy of zero tolerance for harassment. OHBM Brainhack 2021 is intended for everyone to feel safe, learn from each other and share knowledge. Our event would be enriched by your involvement and contributions. To support our mission, please share this widely-we'd especially love your help translating and sharing this message in your local language to reach as many people around the world as we can! Events will take place across two main time slots to support as many time zones as possible. About us: We are the Open Science Special Interest Group (OSSIG) within the Organization for Human Brain Mapping (OHBM) society, which hosts a yearly conference on mapping the brain with neuroimaging. The OSSIG is dedicated to promoting Open Science in this community and neuroscience more broadly. Please contact ohbmopenscience(a)gmail.com <mailto:ohbmopenscience@gmail.com> if you have any questions. Thank you! All the best, Matteo and Tibor On the behalf of the OHBM Open Science SIG

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