Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

03 Aug '20

External Email - Use Caution Hi Freesurfers. There is a "ctx-lh/rh-corpuscallosum" label in Freesurfer, but the Corpus Callosum is not considered to be in the cortex. Can you explain precisely what this label refers to? Thanks, Ian

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Dimension mismatch
by Meike Hettwer 03 Aug '20

03 Aug '20

External Email - Use Caution Dear freesurfer experts I got an error that I don't understand when running mri_glmfit on cortical volume in the right hemisphere. I only have one group and one covariate of interest (+ age and ICV). ERROR: dimension mismatch between y and X. y has 102 inputs, X has 105 rows. I attached the log, fsgd and mtx files. I included 105 subjects and I don't get any errors when running the same command for surface area or cortical thickness. I can run my analysis for cortical volume in the left hemisphere, but not in the right hemisphere. The error message sounds like there is data missing for 3 subjects, but as far as I can see, that is not the case. Thanks a lot for you help, Meike

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mri_aparc2aseg: how to remove redundant output labels?
by Ellen Ji 03 Aug '20

03 Aug '20

External Email - Use Caution Dear experts, I am running mri_aparc2aseg using two annotations as input (one for each hemisphere), each with 159 labels, and wish to end up with a single output segmentation of 318 labels. However, when I run the below, this is not the case: mri_aparc2aseg \ --s subject1 \ --annot 500_sym.aparc \ --wmparc-dmax 2 \ --labelwm \ --hypo-as-wm \ --o subject1/mri/parcellation.nii.gz In fact, the output has 680 labels rather than 318 labels. A few questions. - How can I see what exactly the 680 label names are (how to extract from the .nii.gz output file)? Currently, I have just quantified it to be 680 by doing this in matlab: gunzip('parcellation.nii.gz') a = MRIread('parcellation.nii'); u = unique(a.vol(:)); length(u) % total number of labels - I believe the extra labels are from the Freesurfer LUT. How can I make sure they are not added when running mri_aparc2aseg? (such that only my annotation labels are included in the output) Thank you very much, Ellen ***** Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch homanlab.github.io/ellen/

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Gray matter volume image per group
by Oana Georgiana Rus 03 Aug '20

03 Aug '20

External Email - Use Caution Dear Freesurfer Community, I want to have an image of the average gray matter Volume in each of my 3 groups, and I did not find a good way to do it. I easily obtained an image from the GM thickness and area by using make_average_subject in each of my 3 groups (young musicians, old musicians and old nonmusicians). Thereby in the surf subfolder I could find an image of these 2 measures. Could anybody give some helpful hint. I am using FreeSurfer 6.0 on an Ubuntu Machine.18.04.4 LTS. Best regards, Georgiana

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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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