Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

Post-doctoral Fellowship in Human Perceptual Neuroscience at New York University
by Wu, Yuan hao 31 Jul '20

31 Jul '20

External Email - Use Caution The Perception and Brain Dynamics Laboratory (PI: Biyu J. He, http://www.med.nyu.edu/helab/) at New York University is currently searching for a post-doctoral fellow to study conscious perception and predictive mechanisms in the human brain. We are looking for a candidate with a passion for perceptual and cognitive neuroscience, independent critical thinking, strong analytical and quantitative skills, and good interpersonal skills. Experience with human brain imaging (such as fMRI, E/MEG, or ECoG) and excellent programming skills are highly desirable. Our laboratory is located on the medical campus of New York University in Manhattan, NY, and is affiliated with the Neuroscience Institute, Departments of Neurology and Radiology. The position is expected to start in early 2021. We provide competitive salary and benefits that adjust for cost of living in New York City. To apply, please send a CV, a cover letter, a statement of scientific and career goals, and names and contacts of three referees to Prof. Biyu Jade He (email: biyu.jade.he(a)gmail.com)<mailto:biyu.jade.he@gmail.com)> with the subject line "post-doctoral application 2020".

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Maintain consistency in build stamp patterns
by Billah, Tashrif 31 Jul '20

31 Jul '20

See the build stamp patterns: In versions < 6.0.0: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c In version 7.1.0: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b The latter has "v" missing from the version string that makes it hard for my pipeline to detect FreeSurfer version. Can you include that in future releases? Also, it would help if you can have a VERSION.txt file with just version string in it such as 7.1.0. -Tashrif .

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Re: [Freesurfer] Recon-all Soft Errors
by Elana Sarabin 30 Jul '20

30 Jul '20

External Email - Use Caution Ages 9-10. MRI scans were taken from the Adolescent Behavioural Cognitive Development (ABCD) database. Elana -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: July 30, 2020 10:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 197, Issue 59 [△EXTERNAL] Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FS 7.1.0 - Editing intensity values for WM (Nils B?er) 2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce) 3. Creating .annot file for a mri_decimate downsampeld version of pial surface (Donelson Berger) 4. GONE: -make to recon-all (Johnson, Hans J) 5. Re: fsgd file - glmfit error (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience) 6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.) 7. bad interpreter: No such file or directory error (Hengameh Marzbani) 8. Re: overlapping/ superimposing regions of one analysis over another (Douglas N. Greve) 9. Re: Creating .annot file for a mri_decimate downsampeld version of pial surface (Douglas N. Greve) 10. Re: Recon-all Soft Errors (Douglas N. Greve) 11. Re: Coregistration to MNI (Douglas N. Greve) 12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji) 13. Re: bad interpreter: No such file or directory error (fsbuild) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Jul 2020 21:27:03 +0200 From: Nils B?er <nils.tobias94(a)gmail.com> Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello everyone, I just have a short question, because I can't find anything helpful in the tutorials. In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that. I'd be thankful for any feedback/links to guides. Best regards, Nils -- Nils B?er Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] Coregistration to MNI
by Douglas N. Greve 30 Jul '20

30 Jul '20

It looks like cvs failed. Can you send the log? Also, please remember to post to the list and not us personally. On 7/30/2020 11:13 AM, Camargo, Aldo wrote: > > External Email - Use Caution > > Hi Douglas, > > > I was able to run the script to create the cvs folder and its files > but still I can not run the script that does the coregistration of the > Pet image to the MNI space. > > I am getting the following error: > > (base) > acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46.0/S19445/subj1/mri$ > mri_vol2vol --gcam > /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/meanPET.nii.gz > register.dof6.lta > $SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > $FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 > pet.cvs.2mm.sm00.ni.gz > Loading mov > /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/meanPET.nii.gz > Loading source LTA register.dof6.lta > Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > ERROR: cannot find or read > /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > > > > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* Wednesday, July 29, 2020 10:39 AM > *To:* Camargo, Aldo <ACamargo(a)som.umaryland.edu>; Freesurfer support > list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Coregistration to MNI > Here is the command > mri_cvs_register --mov $subject --mni --openmp N > > This command can take a very long time to run. The --openmp N > indicates the number of processors to use if you have a multiprocessor > system. Even with N=3, it can take 18 hours. > > > > > On 7/29/2020 12:35 AM, Camargo, Aldo wrote: >> >> External Email - Use Caution >> >> Hi Douglas, >> >> I don't have the folder cvs and I don't have the files bellow: >> >> cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z >> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta >> >> How can I get these files, >> >> Aldo >> >> ------------------------------------------------------------------------ >> *From:* Camargo, Aldo <ACamargo(a)som.umaryland.edu> >> <mailto:ACamargo@som.umaryland.edu> >> *Sent:* Monday, July 27, 2020 11:46 PM >> *To:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] Coregistration to MNI >> Thanks a lot Douglas for your great input, >> >> Aldo >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas >> N. Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> >> *Sent:* Monday, July 27, 2020 10:46 AM >> *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> >> *Subject:* Re: [Freesurfer] Coregistration to MNI >> This command will allow you to have a registration file and sample >> into MNI152 2mm space >> >> mri_vol2vol --gcam pet.nii.gz register.dof6.lta >> $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z >> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 >> pet.cvs.2mm.sm00.nii.gz >> >> you can get the registration file with >> mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta >> >> >> >> On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: >>> Hi Aldo, >>> If you have a recon-ned structural MRI corresponding to your PET >>> scan then the answer is yes. >>> Lilla >>> ------------------------------------------------------------------------ >>> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of >>> Camargo, Aldo <ACamargo(a)som.umaryland.edu> >>> <mailto:ACamargo@som.umaryland.edu> >>> *Sent:* Saturday, July 25, 2020 12:19 AM >>> *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* [Freesurfer] Coregistration to MNI >>> >>> External Email - Use Caution >>> >>> Hi Freesurfer experts, >>> >>> I want to coregister a PET image to the MNI space, can I use >>> mri_cvs_register ? >>> >>> Thanks a lot, >>> >>> Aldo Camargo >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto: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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Recon-all Soft Errors
by Elana Sarabin 30 Jul '20

30 Jul '20

External Email - Use Caution Hi Freesurfer experts, I am a first time user of FreeSurfer and I haven’t been able to find any threads for how to fix some of my problems. I have a very large dataset and as I am editing on freeview I am noticing that ½ or more of my participants have a large area missing in the brainmask.mgz file but the region is visible from the T1.file. In some participant scans the areas missing arent too big however other scans (the photo I attached) have a very large portion of the brain missing. I have tried quite a few things to fix this including re running recon-all, adding control points, and adjusting the wsthresh value, however, none have worked. Wondering if there is a way to fix this kind of error and if there is a way to prevent this from happening as I run recon-all on future participants. In addition, I have been duplicating my files before editing in order to always have the original files as a backup. With some participants when I duplicate the files their T1.mgz file ends up completely white (image attached). I have yet to see this in a none duplicated file however with some participants I can duplicate the files and have no issue. I have attached photos of both of my problems. Any suggestions for fixes would be greatly appreciated. Thanks, Elana

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Creating .annot file for a mri_decimate downsampeld version of pial surface
by Donelson Berger 30 Jul '20

30 Jul '20

External Email - Use Caution Hello FreeSurfer Expert, I've run into a problem that I just can't seem to solve. After downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces and 10,002 points, I don't know how to create .annot files for the new surfaces I created. I want to be able to tell which ROI each vertex is in for my new surface based off a parcellation. I've been trying to use mri_ca_label, mri_ca_train, and mris_sample_parc, but I can't seem to get anything to work. Do you have any suggestions? Thanks for your help, Donelson Graham Berger

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overlapping/ superimposing regions of one analysis over another
by Sunil Khokhar 30 Jul '20

30 Jul '20

External Email - Use Caution Dear Experts, I have done a between group (2 groups) difference in whole brain voxel based cortical thickness using QDEC, which showed significant regional differences in certain clusters bilaterally in the brain. I also did a correlation between cortical thickness and behavioral scores separately in these two groups. Now, I want to superimpose regions (clusters) which showed positive and negative correlation on the results/ regions I obtained in my between group analysis. How can I do this? Thanks in advance! Sunil. _______________ Sunil K Khokhar PhD Scholar, Department of Neuroimaging & Interventional Radiology, NIMHANS, Bengaluru, INDIA. khokharsunil1(a)gmail.com +91-9413101839

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bad interpreter: No such file or directory error
by Hengameh Marzbani 30 Jul '20

30 Jul '20

External Email - Use Caution Hello Freesurfer developers, I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command. However,I have tried to run recon-all. but, I have got the following error message on all PCs: *bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory* also The build-stamps.txt file contents: *freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b* Thank you in advance, Best regards, Hengameh

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fsgd file - glmfit error
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 29 Jul '20

29 Jul '20

External Email - Use Caution Dear Freesurfer experts, Hope this email finds you well. I am having some trouble with the fsgd file for glmfit and I'm confused why. This is the error I'm getting when running glmfit: iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir gdfRead(): reading fsgd_8.fsgd ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) iMac-Pro:BAP_complete ajobsaid$ If needed, I can send you my fsgd file, but I have triple checked the design and format of the file (it is saved as .fsgd), and I'm still getting this error message. Thank you, Alex

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GONE: -make to recon-all
by Johnson, Hans J 29 Jul '20

29 Jul '20

External Email - Use Caution The release notes for 7.0.0 claim that the -make option is "Gone" from recon-all. This option, however, is still available and does not seem to fail. I am running several thousand data sets on a cluster through Freesurfer 7.1.0, and periodically the process fails for some subjects. In the past the "recon-all -make all" feature was a very convenient way to complete freesurfer runs that were terminated early for some unknown reason Q1) should "recon-all -make all" be avoided for FreeSurfer 7.1.0? Q2) is there an alternate way to "continue form the point where results are missing" in the pipeline? Thanks, Hans

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Freesurfer July 2020