Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

100 participants
144 discussions

Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 15 Aug '19

15 Aug '19

External Email - Use Caution Dear Doug, Here is the emails: Message: 6 Date: Fri, 2 Aug 2019 01:55:34 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"? To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <183e8a60-1cc2-1680-26a7-bce8a1d03315(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" If you look in the recon-all.log file for any subject, you will see a mri_aparc2aseg command line. YOu can use that specifying your annot and the new output name. On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote: External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels: mri_aparc2aseg --s subject name --annot annotation name --o output name and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not?? Any help would be appreciated. Regards, Mahshid

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mri_vol2surf error
by Pratik Kashyap 14 Aug '19

14 Aug '19

External Email - Use Caution mri_vol2surf --cortex --hemi lh --interp trilinear --o rest2.nii.gz --out_type niigz --reg register.dat --projfrac-avg 0.500 --mov rest2.nii --surfreg sphere.reg --trgsubject fsaverage A source volume path must be supplied Hey, I'm running the above command, getting an error 'A source volume path must be specified' I checked all the source paths, they exist. But the output path doesn't , which is weird as it isn't a source path. Please help, PK

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multimodal analysis (pet and cortical thickness relationship) using --pvr
by miracle ozzoude 14 Aug '19

14 Aug '19

External Email - Use Caution Hello Experts, I am performing an analysis looking at the relationship between amyloid uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups and 2 variables (age and education). I want to run a within group analysis while regressing out age and education (i.e. Within group 1, is there a negative relationship between amyloid uptake and cortical thickness regressing out the effects of age and education). However, i'm not sure how my pvr contrasts will look like. Below are my fsgd and an attempt at creating contrasts. Please, can you let me know if my contrasts are correct based on my questions. Thank you. Best, Paul The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship Amy-thick reg out age and education Class g1 Class g2 Variable Age Education Input XX1 g1 60 16 Input XX2 g1 58 14 Input YY1 g2 62 20 Input YY1 g2 62 20 ------------------------------------------------------------- matrix for group1: pvrgroup1= 1 0 0 0 0 0 0 is there a relationship between amyloid-thickness in group1 regressing out age and education? matrix for group2: pvrgroup2= 0 1 0 0 0 0 0 is there a relationship between amyloid-thickness in group2 regressing out age and education?

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Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 14 Aug '19

14 Aug '19

External Email - Use Caution Dear Doug, Thanks for your reply. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt" which used a predefined file from freesurfer folder. Actually, I used the mri_aparc2aseg command with some changes, seen bellow: mri_aparc2aseg --s mysubj --annot aparc --o $SUBJECTS_DIR/mysubj/mri/parc.mgz so, I am wondered if it reads the ' /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I would appreciate it of you could help on. Regards, Mahshid

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Questions about pial surfaces segmentation
by Hsin-Hung Li 14 Aug '19

14 Aug '19

External Email - Use Caution Hello FreeSurfer Developers, I run recon-all on the T1 and T2 images of a few new human subjects. After running recon-all, I followed the freesurfer troubleshooting tutorial, and started visually checking the segmentation of the pial surfaces and white surfaces. I found similar errors among a few subjects, and would like to make sure that what I am thinking is correct before proceeding: The figures I attached are the coronal view of the same subject (from the left column to the right column: posterior to anterior). These errors mainly occurred at the occipital cortex, and at the boundary between the left and right hemisphere. It seems that the pial surface included a piece of dura matter that should not be there. It is indicated by the green arrows in the images. It also seems to happen at the places indicated by the blue arrows, but not as visible. Is what I'm thinking correct? I also attached an image containing three different views of the same subject. In general, will running -gcut in this example help reducing the errors above? -The recon-all is run on a server with freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -uname -m x86_64 -recon-all.log: see attached Thank you so much. HHL

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Re: [Freesurfer] Help with MRI segstats
by Greve, Douglas N.,Ph.D. 14 Aug '19

14 Aug '19

Can you send a command line and terminal output with the error? On 8/14/19 9:38 AM, Daliah Ross wrote: > > External Email - Use Caution > > Hello, > > I have tried using just one of the arguments, but I'm still not > getting my desired output. I'm not sure if I've explained my question > correctly. I am looking to get anatomical labels on the clusters that > I've already created through mri_surfcluster to find out where in the > cortex each cluster is. How would I go about doing this? I was hoping > that mri_segstats could give an output where it lists each cluster > starting with the biggest and where it is located. I've been able to > get this list, but without anatomical labels. I appreciate your help! > > Thank you, > Daliah > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > > On Thu, Aug 8, 2019 at 8:01 PM Daliah Ross <dross3(a)mail.yu.edu > <mailto:dross3@mail.yu.edu>> wrote: > > Hi, > > No, we primarily wanted this for the un-permuted case, to be able > to identify the anatomical regions for each cluster. In addition, > we have thought about looking at the spatial cluster distribution > for the permutations to see if there are any regions which are > more prone to false positives, which might be indicative of e.g. > parcellation or imaging issues, but we haven’t yet figured out how > to best go about that step. And, yes, for the permutations we are > running mri_surfcluster and extracting the max cluster size per > permutation. Thank you for the advice! > > Daliah > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > > On Wed, Aug 7, 2019 at 4:51 PM Greve, Douglas N.,Ph.D. > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: > > You should only pass one of --seg, --annot, or --slabel to > mri_segstats. I don't understand how you are trying to use > this in the > context of your permutation. Is this something that you are > running on > each iteration? If so, it is probably not what you want to do. > Probably > you want to run mri_surfcluster to get the cluster sizes out. > > On 8/7/19 1:31 PM, Daliah Ross wrote: > > > > External Email - Use Caution > > > > This is the command line: > > mri_segstats --seg F_lhstats_6covars_ > sm5_Interaction_negNumCl_F7.mgh > > --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex > --sum > > F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt > > > > We are running the permutations within FS, but because our > model is a > > linear mixed model, and we didn't think that this would be > compatible > > with fspalm. So, we are running the permutations "manually" > (i.e. we > > are generating the random permutations, which in our case is > just > > switching the subject labels for the thickness data. We are > then using > > mri_surfcluster to extract the maximum cluster size per > permutation > > and will use the permutation distribution to determine our the > > statistical significance of our results). In addition, our > analyses > > are a bit out of the ordinary in that the thickness data are an > > independent variable in our model, for which we have a repeated > > non-imaging measure as the outcome. Effectively, we are > using the > > thickness maps to generate vertex-wise regressors, with a fixed > > outcome measure (fixed in the sense that it doesn't vary > across the > > brain). > > > > If you have any thoughts about how we could use fspalm in > our case, > > your advice would be most appreciated. > > > > Thanks again, > > Daliah > > > > *Daliah Ross* | dross3(a)mail.yu.edu > <mailto:dross3@mail.yu.edu> <mailto:dross3@mail.yu.edu > <mailto:dross3@mail.yu.edu>> > > > > Ph.D. Student, Clinical Psychology with Health Emphasis > > Ferkauf Graduate School of Psychology > > Yeshiva University > > Albert Einstein College of Medicine > > > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > <mailto:freesurfer-bounces@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> > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> On Behalf Of > > Greve, Douglas N.,Ph.D. > > Sent: Tuesday, August 6, 2019 12:56 PM > > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Subject: Re: [Freesurfer] Help with MRI segstats > > > > Can you send command lines? Also, are you using the built-in > > permutation tool or trying to do something outside of FS? > > > > On 8/6/19 8:40 AM, Daliah Ross wrote: > > > > > > External Email - Use Caution > > > > > > Hi FreeSurfer experts, > > > > > > I have a couple of questions regarding mri_segstats > tool for an > > > analysis on vertex-wise cortical thickness data. We are > > attempting to > > > compare maximum cluster sizes among permutations. We > are having > > > trouble figuring out how to get the anatomical label > for each > > cluster > > > using the --slabel argument. We are also wondering if the > > difference > > > between cluster sizes between mri_surfcluster and > mri_segstats > > is due > > > to partial volumes, and if so, how to correctly use > the --pv > > argument. > > > It suggests in the wiki page that mri/norm.mgz volume > is usually > > used > > > but I believe we need something surface-based since we > are using > > > thickness data. > > > > > > Thank you in advance for any help you can provide. > > > > > > Best, > > > Daliah > > > > > > *Daliah Ross* | dross3(a)mail.yu.edu > <mailto:dross3@mail.yu.edu> <mailto:dross3@mail.yu.edu > <mailto:dross3@mail.yu.edu>> > > <mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu> > <mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu>>> > > > > > > Ph.D. Student, Clinical Psychology with Health > Emphasis Ferkauf > > > Graduate School of Psychology Yeshiva University > Albert Einstein > > > College of Medicine > > > > > > _______________________________________________ > > > 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 <http://nmr.mgh.harvard.edu> > > > <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C0 > > > 1%7Cmark.wagshul%40einstein.yu.edu > <http://40einstein.yu.edu> > > > <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2% > > > > > > 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654&sd > > > > ata=ALndUpHJ%2BYhuMzChviSn9ygf8H112mUKvVmJktGoqB4%3D&reserved=0 > > > > > > _______________________________________________ > > 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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… > > > > > > 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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Gender and age based reconstruction
by Carissa Liana Grijalva 14 Aug '19

14 Aug '19

External Email - Use Caution Hello, I reached out the other day about if there was a way to specify the data is from a specific gender or age during the recon all code, such as a tag at the end. I was told that there is not way to tell recon-all about demographics/subject meta data, and not to worry about this during recon-all, but instead add age and gender as covariates in the model later. Does this mean FreeSurfer automatically finds the right regions regardless of age or gender? Does this work based on gray/white matter thresholds or something similar, so regardless of the demographics of the brain, it find the right regions? Thank you for your time. Best, Carissa Grijalva -- *Carissa Grijalva* *University of Arizona * *Biomedical Engineering PhD Program* *Undergraduate Research Opportunities Consortium Scholar* *NSF WAESO Research Fellow* *Society of Hispanic Professional Engineers*

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nu_correct error
by Z Hessam 14 Aug '19

14 Aug '19

External Email - Use Caution Hello Dear FreeSurfer Developers, I'm attempting to run some of data with recon-all code, and after some success run on several data, now I get the following error message even when I run those data that ran well before: nu_evaluate: crashed while running evaluate_field (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Linux ubuntu 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux I couldn't find any solution in previous emails, and the output of these 2 commands: 1) echo $FREESURFER_HOME 2) ls -l $FREESURFER_HOME/mni/bin/nu_correct were: 1)/media/hessam91/driver2/freesurfer 2)-rwxrwxrwx 1 8481 1590 20569 Jun 19 2015 /media/hessam91/driver2/freesurfer/mni/bin/nu_correct what can I do to solve this problem? thank you so much

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asegstats2table error - measure 63 expected 66
by Fernanda Hansen P. de Moraes 13 Aug '19

13 Aug '19

External Email - Use Caution Dear Freesurfer experts, We had just reprocessed our subjects with the -long flag fr the longitudinal processing, and when extracting volumes with asegstats2table I have the following error: WARN: SUBJ229_ses-1.long.SUBJ229_tmpl nmeasures = 63, expecting 66 for all our subjects on the list. I just found this older message about the same error ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036502.ht… ), and I am now looking for the subject with 66 ROIs. However, for now, all of then present 45 ROIs. Is there any suggestion on how can we trespass this error? Regards, -- Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Research Assistant Job Opening
by Prakash Lab 13 Aug '19

13 Aug '19

External Email - Use Caution Hello, The Ohio State Clinical Neuroscience Laboratory directed by Dr. Ruchika Prakash is seeking to hire a Research Assistant (RA). Please see attached document for full description. Best Regards, The Clinical Neuroscience Laboratory [image: The Ohio State University] Lab Manager The Clinical Neuroscience Laboratory Department of Psychology 74 Psychology Building, 1835 Neil Avenue, Columbus, OH 43210 614-292-9568 Office ra(a)clinicalneurosciencelab.com www.clinicalneurolab.org Confidentiality Notice: This email transmission (including any documents, files or attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, you are hereby notified that any disclosure, copying or distribution, or any use of the enclosed or attached information is strictly prohibited. If you have received this transmission in error, please notify me immediately by return email and delete all materials without reading, copying, saving or printing them.

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Freesurfer August 2019