Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Re: [Freesurfer] RBV PVC
by Nathalie Mertens 19 Aug '20

19 Aug '20

External Email - Use Caution Dear, I am not sure if the questions below were sent correctly to you, since I did not receive any copy of it. Please find my message below. Many thanks, looking forward to your reply. Kind regards, Nathalie Mertens Van: Nathalie Mertens <nathalie.mertens(a)kuleuven.be> Datum: dinsdag 18 augustus 2020 om 09:33 Aan: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Onderwerp: RBV PVC Dear, I do have some questions linked to RBV PVC implemented in Freesurfer: 1. Could you please tell me how the RBV PVC is acquired? Is the RBV PVC acquired based on Muller-Gartner (on a region-level, and based on only using gray- versus white matter), or when and how are the different regions from gtm_seg applied to obtain GTM? 2. What would be the advantage of using your technique compared to for instance sGTM? 3. Could you please tell me the difference in region-definition between aparc+aseg and the gtm_seg? (I saw that the latter contains less regions compared to aparc+aseg.) What is the reason to use the latter compared to the aparc+aseg, based on the definitions of the regions? (I know that gtm_seg is used which has a high resolution, but not quite sure, apart from the resolution, why you are not using aparc+aseg for the RBV PVC.) 4. Is there a mask applied to the gtm_seg to exclude regions that are located outside the brain? Many thanks for your answers. Kind regards, Nathalie

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" quantifyThalamicNuclei.sh" commend does not work..
by Haewon Roh 19 Aug '20

19 Aug '20

External Email - Use Caution Hi team. I'd like to collect all kinds of volumes of subjects' thalamic nuclei but the command " quantifyThalamicNuclei.sh" does not work in my mac book's terminal window. (there's no error message but any file was not made after that command ; please find attached screenshot showing the this problem) Before doing that command on terminal window, I made sure that every subject file had three files (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes) after the process of segmenting thalamus. But, for hippocampal and amygdala subsegmentations, command of "quantifyHAsubregions.sh" is working well.. What is the difference between thalamic nuclei and hippoamygdala substructures for gathering all volumes into tabelfile ? my subjects were preprocessed with freesurfer version 6.0 and their substructure segmentations were made using freesurfer version 7.1. Does this make this problem? I attached screenshot of my terminal window as below.. Thank you always !! -- Hae Won ROH, M.D. H.P: +82-10-4341-8142 E-mail: rofree1st(a)gmail.com

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Developer password
by Miglius Mikalauskas 19 Aug '20

19 Aug '20

External Email - Use Caution Hello, Maybe you can help me. I have followed the freesurfer installation guide with virtual box and ubuntu, but i was not able to log in. Maybe you could send me the password. I saw that people were writing because of the same in the mail archive and they were answered that the password should be sent to their email. I am not sure where to ask for the password.

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fs7..1.1 and age range
by Alexopoulos, Dimitrios 18 Aug '20

18 Aug '20

External Email - Use Caution Is 7.1.1. still considered to be best used as a pipeline for subjects older than ~5yo? Have any parts of the infant pipeline been incorporated so that it be used for babies or subjects up to 2yo, or do we still need to run separate infant pipeline? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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-fill-ribbon command.
by Thomas Alderson 18 Aug '20

18 Aug '20

External Email - Use Caution Dear Freesurfer experts, Although this issue was raised in the archive, I could not find an answer. I want to create a 3d volume using an annot file. I run the following command. 'mri_label2vol --annot $SUBJECTS_DIR/' subj '/label/lh.Schaefer2018_100Parcels_7Networks_order.annot --temp $SUBJECTS_DIR/' subj '/mri/orig.mgz --identity --fillthresh .3 --subject ' subj ' --hemi lh --o $SUBJECTS_DIR/' subj '/schaefer_volume_left.nii.gz --proj frac 0 1 .1' This produces a 3d volume but the ribbon is not well filled (it's patchy and extends outside the ribbon). I tried to use --fill-ribbon but this produces a binary volume of the ribbon without the label information from my annot file. How can I convert my annot into a 3d volume that completely fills the ribbon and retains label information? Thank you. -Tom.

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Re: [Freesurfer] Queries regarding installation of FreeSurfer software
by fsbuild 17 Aug '20

17 Aug '20

External Email - Use Caution Hello Dharmendra, It looks like you are trying to move the “..license” file out of the Applications folder using "sudo mv"- but the password is not being accepted ?  You will need to know the admin password to use the sudo command. What version of freesurfer are you using ? - older versions use a “.license” file under $FREESURFER_HOME.   Instead of using the "mv" command, you can copy "cp" your existing license file to another freesurfer distribution if you like - no need to remove it by using the “mv” command. But I believe you would still need to know the sudo password to use "cp" if you needed it for "mv". - R. On Aug 14, 2020, at 02:55, Dharmendra Jakhar <d.jakhar2014(a)gmail.com> wrote:        External Email - Use Caution        I, Dharmendra Jakhar, a researcher working on brain mapping and an aspiring user of your software, is facing difficulties in installation of FreeSurfer software. Query 1-We have duly downloaded and installed the directory in the application folder, but we are getting a prompt in the terminal that 'No such file or directory is found'. We have attached the screenshot for your reference.Query 2-We are also not able to type License key password instead in its place we can see a 'key symbol'. We have also attached the screenshot for your reference. <Query_1_screenshot.png><Query_2_screenshot.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FS edits of subcortical parcels
by Alexopoulos, Dimitrios 17 Aug '20

17 Aug '20

External Email - Use Caution FS editing experts, I have a subject with enlarged ventricles and processed the subject with recon-all -bigventricles flag. The surfaces look good but the subcortical segmentation and some WM around the ventricles , especially for the right hem, are poor. Images below. What is the best approach to edit this segmentation? There are some WM edits required and some caudate, lentiform edits as well. Is the aseg or aseg+aparc edited? Jim [cid:image001.jpg@01D6718F.CD2B0920] [cid:image002.jpg@01D6718F.CD2B0920] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] surf2vol from annotation?
by Douglas N. Greve 17 Aug '20

17 Aug '20

On 8/13/2020 10:15 AM, Ellen Ji wrote: > > External Email - Use Caution > > Thanks Douglas. > > recon-all was performed using FS V6. However, we have since upgraded > to V7. Should I stick with what was originally used (mri_aparc2aseg)? > I don't think it will make much of a difference, so do whatever is easier for you > > Here is how the wmparc.mgz was created. Could you verify if my > modified steps below make sense? > > wmparc.mgz: > > mri_aparc2aseg \ > --s subject1 \ > --labelwm \ > --hypo-as-wm \ > --rip-unknown \ > --volmask \ > --o mri/wmparc.mgz \ > --ctxseg aparc+aseg.mgz \ > > modification for my annotation: > > The reason why I added wmparc-dmax 2 is because I want to extend the > annotation, which only includes gm, into the wm. However, when I do > this, there are 2x the labels (gm and wm). Is there any way to do an > extension while maintaining 318 regions? (if I remove the labels post > hoc using mri_binarize, I believe that would just erase all wm, which > isn't what I want). > > mri_aparc2aseg \ > --s subject1 \ > --annot 500_sym.aparc \ > --wmparc-dmax 2 \ > --labelwm \ > --hypo-as-wm \ > --o subject1/mri/aparc.500+2mm.nii.gz > > Why are you not including --rip-unknown and --volmask? The number of regions is as expected because it labels cortex as well as the adjacent WM, but the adjacent WM gets a different segmentation index. You can merge them back together afterwards if you want. > > best, > > Ellen > > On 8/13/2020 3:39 PM, Douglas N. Greve wrote: >> You can look in the recon-all.log file to see how wmparc.mgz is >> created. Which version of FS are you using? If V6, then the command >> will be mri_aparc2aseg. If V7, then it will mri_surf2volseg. Either >> way, modify the command to use your annotation. >> >> On 8/12/2020 5:18 AM, Ellen Ji wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer experts, >>> >>> I have a surface parcellation (annotation) with 318 labels; see >>> attachments for each hemi. I wish to extract volume-based features >>> (FA and MD) corresponding to these 318 labels. I believe I should >>> perform something like surf2vol to extend the labels into FA space. >>> However, my surface parcellation is not a surface overlay (which I >>> need for --so). Any other ways to do this? >>> >>> I wish for the output to be a single volume-based parcellation of >>> 318 labels, corresponding to the two surface parcellation annotation >>> files. I will then use this output to get FA measures for each of >>> the 318 regions. >>> >>> Thank you, >>> Ellen >>> >>> >>> >>> --- >>> Ellen Ji, PhD >>> Postdoctoral Research Fellow >>> Psychiatric University Hospital >>> University of Zürich >>> ellen.ji(a)bli.uzh.ch >>> homanlab.github.io/ellen/ >>> >>> >>> _______________________________________________ >>> 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] Recon-all Soft Errors
by Elana Sarabin 17 Aug '20

17 Aug '20

External Email - Use Caution Here is the recon-all.log file. Thanks, 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> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/4… ------------------------------ Message: 2 Date: Wed, 29 Jul 2020 20:32:34 +0000 From: "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB660985EC505DEECB596362ADEF700(a)BL0PR04MB6609.namprd04.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hi Nils There are expert options for this. You can specify things like -min_white 90 to some of the programs like mri_segment and the surface placement stuff Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Nils B?er Sent: Wednesday, July 29, 2020 3:27 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM 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<mailto:nils.tobias94@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://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<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…> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/a… ------------------------------ Message: 3 Date: Wed, 29 Jul 2020 15:51:03 -0500 From: Donelson Berger <donelsongrahamberger(a)gmail.com> Subject: [Freesurfer] Creating .annot file for a mri_decimate downsampeld version of pial surface To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/d… ------------------------------ Message: 4 Date: Wed, 29 Jul 2020 22:22:47 +0000 From: "Johnson, Hans J" <hans-johnson(a)uiowa.edu> Subject: [Freesurfer] GONE: -make to recon-all To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9DB20083-D647-47E0-9396-C24308B503B9(a)uiowa.edu> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/f… ------------------------------ Message: 5 Date: Wed, 29 Jul 2020 15:49:44 -0700 From: "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn(a)email.gwu.edu> Subject: Re: [Freesurfer] fsgd file - glmfit error To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you Douglas! On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: > Try putting 1 after GroupDescriptorFile, ie, > > GroupDescriptorFile 1 > > On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, > Lab of Autism and Developmental Neuroscience wrote: > > External Email - Use Caution > Here is my fsgd file. > Thank you! > > > On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve > <dgreve(a)mgh.harvard.edu> > wrote: > >> Please send the fsgd file >> >> On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, >> Lab of Autism and Developmental Neuroscience wrote: >> >> 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 >> >> _______________________________________________ >> Freesurfer mailing >> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma >> ilman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai > lman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/2… ------------------------------ Message: 6 Date: Thu, 30 Jul 2020 09:34:12 +0000 From: "Zollei, Lilla,Ph.D." <LZOLLEI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all Soft Errors To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DM6PR04MB44127C2DB157BB07AB669F41E3710(a)DM6PR04MB4412.namprd04.prod.outlook.com> Content-Type: text/plain; charset="windows-1252" Hi Elena, What is the age range of your subjects? Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Elana Sarabin <elana.sarabin1(a)ucalgary.ca> Sent: Wednesday, July 29, 2020 11:02 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all Soft Errors 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 ? 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/d… ------------------------------ Message: 7 Date: Thu, 30 Jul 2020 17:49:49 +0430 From: Hengameh Marzbani <marzbani91(a)gmail.com> Subject: [Freesurfer] bad interpreter: No such file or directory error To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/4… ------------------------------ Message: 8 Date: Thu, 30 Jul 2020 10:20:07 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <c4e336e0-b3b8-89eb-e59b-1894fdf856b8(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" To obtain the common regions, first binarize the clusterwise significance maps with something like mri_binarize --min 2.0 --i clustersigmap1.mgh --o bin.clustersigmap1.mgh Same for the other groups Then take the intersection fscalc clustersigmap1.mgh and clustersigmap2.mgh -o intersection.mgh On 7/27/2020 2:17 PM, Sunil Khokhar wrote: > > ????????External Email - Use Caution > > To operate the visualization and obtain the common regions of my > between-group difference results and the correlation results in one > image. In other?words, overlapping/ superimposing?my correlation > results on the between-group results (to obtain the common regions > from the two separate analysis). > > Thanks > _______________ > Sunil K Khokhar > PhD Scholar, > Department of Neuroimaging & Interventional Radiology, NIMHANS, > Bengaluru, INDIA. > khokharsunil1(a)gmail.com <mailto:khokharsunil1@gmail.com> > +91-9413101839 > > > On Mon, Jul 27, 2020 at 8:21 PM Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > are you asking how to create positive and negative regions or are > you asking how to operate the visualization? > > On 7/25/2020 9:40 AM, Sunil Khokhar wrote: >> >> ????????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 <mailto:khokharsunil1@gmail.com> >> +91-9413101839 >> >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/7… ------------------------------ Message: 9 Date: Thu, 30 Jul 2020 10:21:14 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Creating .annot file for a mri_decimate downsampeld version of pial surface To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <ec2eef74-6cd8-0c36-dbeb-983240090223(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Use mris_apply_reg --sval-annot lh.your.annot --streg lh.pial lh.pial.decimated --o lh.your.decimated.annot On 7/29/2020 4:51 PM, Donelson Berger wrote: > > ????????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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/e… ------------------------------ Message: 10 Date: Thu, 30 Jul 2020 10:26:22 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all Soft Errors To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" for the first error, can you send the recon-all.log file? For the second error, you need to adjust the intensity ranges. For some reason they are coming up as 0s. On 7/29/2020 11:02 AM, Elana Sarabin wrote: > > ????????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 ? 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/5… ------------------------------ Message: 11 Date: Thu, 30 Jul 2020 11:31:47 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Coregistration to MNI To: "Camargo, Aldo" <ACamargo(a)som.umaryland.edu>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9af8c73e-46a8-e9b6-4b84-ce507589efed(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" 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/me > anPET.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/me > anPET.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. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/d… ------------------------------ Message: 12 Date: Thu, 30 Jul 2020 17:39:06 +0200 From: Ellen Ji <ellen.ji(a)bli.uzh.ch> Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output labels? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <24cc8874-81ee-1e68-85ad-b8fe662c4fc3(a)bli.uzh.ch> Content-Type: text/plain; charset="utf-8"; format="flowed" 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 Z?rich ellen.ji(a)bli.uzh.ch homanlab.github.io/ellen/ ------------------------------ Message: 13 Date: Thu, 30 Jul 2020 17:48:25 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] bad interpreter: No such file or directory error To: freesurfer(a)nmr.mgh.harvard.edu Cc: marzbani91(a)gmail.com Message-ID: <1596124105.5f22ebc98f04a(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Hengameh, You probably need to install tcsh (and or csh). I would try, $ sudo apt-get install csh tcsh - R.. On Jul 30, 2020, at 09:19, Hengameh Marzbani <marzbani91(a)gmail.com> wrote:        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 directoryalso The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, Hengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/8… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 197, Issue 59 *******************************************

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mri_vol2vol
by 侠义江湖，醉笑人生 17 Aug '20

17 Aug '20

External Email - Use Caution Hi, freesurfer experts. I am running dt_recon and mri_vol2vol to obtain FA values of ROI. Everything is OK after running the dt_recon command. But some subjects in my study show an issue with mri_vol2vol registration. When checking the wmparc2diff.mgz I created, it is apparent that surfaces of lh.white and rh.white are not mismatched with the wmparc2diff.mgz. This issue is also mentioned by another user. The Web link is https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55788.html.&… Could you give me some advice? Thanks. He Tao

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