Freesurfer

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Re: [Freesurfer] mri_vol2vol and diffusion issue
by 真我 10 Aug '20

10 Aug '20

External Email - Use Caution Hi, Dr. Greve.   I am sorry to reply so late. The version of FS I used is v6.0.0. Here are the dt_recon and recon_all file. Thanks. Bo Tao ------------------ Original ------------------ From: "freesurfer" <freesurfer-request(a)nmr.mgh.harvard.edu>; Date: Fri, Aug 7, 2020 10:18 PM To: "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Freesurfer Digest, Vol 198, Issue 11 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. Re: labels in .nii file (Douglas N. Greve)    2. Re: high pass filter cutoff (Douglas N. Greve)    3. Re: Recon-all Soft Errors (Douglas N. Greve)    4. Re: mri_vol2vol and diffusion issue (Douglas N. Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 7 Aug 2020 10:10:43 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] labels in .nii file To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <95d0a55e-80c2-915c-caf3-e45af6c8a9c1(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" The hemi just refers to either lh or rh to load the proper surface. The command have no idea what you are transferring to the surface. Before the mri_vol2label stage, try loading surf.MDROI? onto the surface as an overlay and see if the ROIs are showing up in the right place On 8/6/2020 11:41 AM, Eleni Nikalexi wrote: > > ????????External Email - Use Caution > > Dear Freesurfer developers, > We have a volume that assigns unique numerical labels to each of the > ROIs it contains, in NIFTI format. I want to register it to MNI152 > (1mm) space, so that I can map it on my subjects and use > mris_anatomical_stats. > I have tried the following command: > > 1. tkregisterfv --mov MDROI.nii --s MNI_1mm --regheader --reg > registrationMD/MDROI.lta > > to get : ?"LTA input is not RAS to RAS...converting...". > Then I run: > > ????????2. mri_vol2surf --src MDROI.nii --src_type nii --out > registrationMD/surf.MDROI.mgh --reg > ????????????registrationMD/MDROI.lta --hemi lh?--surf white > --projdist-max 0 1 0.1 > ? ? ?3. mri_vol2surf --src MDROI.nii --src_type nii --out > registrationMD/surf.MDROI_rh.mgh --reg > ????????????registrationMD/MDROI.lta --hemi rh?--surf white > --projdist-max 0 1 0.1 > The 2 commands above demand the --hemi argument, but I wasn't sure > what to put, as the ROIs are mixed and are in both hemispheres. Thus I > run the command once for the left and once for the right hemisphere, > creating different .mgh files. > Last, I continued with: > > ? ? ? ? 4. mri_vol2label --i registrationMD/surf.MDROI.mgh --id 1 --l > lab.MDROI_lh.label --surf MNI_1mm l > > which failed, as I get "ERROR: found no voxels matching id 1" > > Could you please tell me, if the commands make sense, and if I should > change something? > > Thank you so much for your help! > > Best regards, > Eleni > > _______________________________________________ > 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/20200807/1… ------------------------------ Message: 2 Date: Fri, 7 Aug 2020 10:15:01 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] high pass filter cutoff To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <d1c723ac-8baa-af79-5812-fcffae6eaacb(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"; format=flowed There is not a hard and fast formula. With a block length of 16 sec, you will have frequencies at 0.0625Hz and multiples thereof. The closer you are to 0.625, the more signal you are going to lose. Also, if you don't remove the whitening, then FSFAST will compute a highpass filter for you. I think that .01Hz is probably fine, but you could bump it up to .02Hz too On 8/6/2020 6:11 PM, Nasiriavanaki, Zahra wrote: > Hi Freesurferers > > Could you please let me know how I should calculate the high pass filter cutoff? I have seen a bunch of different formulas (i.e 1.5*the stimulation period)? > My task is a block-designed task, each stimuli takes 16 seconds and is followed by the next stimuli without an ITI. TR=2, number of conditions=8. > I have used a hpf=0.01, Is this correct? > > Thanks > Mona > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 3 Date: Fri, 7 Aug 2020 10:17:42 -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: <80109940-d6ff-33f5-faff-d836725e829b(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" This error shows a massive failure. Is this what you are describing as: includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. On 8/6/2020 9:00 PM, Elana Sarabin wrote: > > ????????External Email - Use Caution > > Here is one photo. Seems this is the most I can send at once. Most > errors look just like this however sometimes larger and sometimes smaller. > > Best, > > Elana > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Douglas > N. Greve" <dgreve(a)mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Tuesday, August 4, 2020 at 8:01 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Recon-all Soft Errors > > [?EXTERNAL] > > Can you send a picture of the type of errors you are seeing? > > On 7/31/2020 9:03 AM, Elana Sarabin wrote: > >      ??????? External Email - Use Caution > >     Here is the recon-all.log file. > >     Thanks, > >     Elana > >     -----Original Message----- > >     From: Elana Sarabin > >     Sent: July 30, 2020 10:21 AM > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Subject: Re: Recon-all Soft Errors > >     Here is the recon-all.log file. > >     Thanks, > >     Elana > >     -----Original Message----- > >     From: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>  On Behalf Offreesurfer-request(a)nmr.mgh.harvard.edu  <mailto:freesurfer-request@nmr.mgh.harvard.edu> > >     Sent: July 30, 2020 10:00 AM > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Subject: Freesurfer Digest, Vol 197, Issue 59 > >     [?EXTERNAL] > >     Send Freesurfer mailing list submissions to > >              freesurfer(a)nmr.mgh.harvard.edu  <mailto:freesurfer@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  <mailto:freesurfer-request@nmr.mgh.harvard.edu> > >     You can reach the person managing the list at > >              freesurfer-owner(a)nmr.mgh.harvard.edu  <mailto:freesurfer-owner@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>  <mailto:nils.tobias94@gmail.com> > >     Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID: > >              <CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw(a)mail.gmail.com>  <mailto:CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw@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@gmail.com  <mailto:nils.tobias94@gmail.com>  /nboeer(a)mail.uni-paderborn.de  <mailto:nboeer@mail.uni-paderborn.de>  <nils.tobias94(a)gmail.com>  <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://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> > >     <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… > >     Virenfrei. > >     www.avast.com  <http://www.avast.com> > >     <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… > >     <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > >     -------------- next part -------------- > >     An HTML attachment was scrubbed... > >     URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/202007… > >     ------------------------------ > >     Message: 2 > >     Date: Wed, 29 Jul 2020 20:32:34 +0000 > >     From: "Fischl, Bruce"<BFISCHL(a)mgh.harvard.edu>  <mailto:BFISCHL@mgh.harvard.edu> > >     Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM > >     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> > >     Message-ID: > >              <BL0PR04MB660985EC505DEECB596362ADEF700(a)BL0PR04MB6609.namprd04.prod.outlook.com>  <mailto:BL0PR04MB660985EC505DEECB596362ADEF700@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@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 Nils B?er > >     Sent: Wednesday, July 29, 2020 3:27 PM > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@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@gmail.com  <mailto:nils.tobias94@gmail.com>  /nboeer(a)mail.uni-paderborn.de  <mailto:nboeer@mail.uni-paderborn.de><mailto:nils.tobias94@gmail.com>  <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://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&ut… <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… > >     Virenfrei.www.avast.com  <http://www.avast.com><https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&ut… > >     -------------- next part -------------- > >     An HTML attachment was scrubbed... > >     URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/202007… > >     ------------------------------ > >     Message: 3 > >     Date: Wed, 29 Jul 2020 15:51:03 -0500 > >     From: Donelson Berger<donelsongrahamberger(a)gmail.com>  <mailto:donelsongrahamberger@gmail.com> > >     Subject: [Freesurfer] Creating .annot file for a mri_decimate > >      ??????? downsampeld???? version of pial surface > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID: > >              <CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA(a)mail.gmail.com>  <mailto:CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA@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/202007… > >     ------------------------------ > >     Message: 4 > >     Date: Wed, 29 Jul 2020 22:22:47 +0000 > >     From: "Johnson, Hans J"<hans-johnson(a)uiowa.edu>  <mailto:hans-johnson@uiowa.edu> > >     Subject: [Freesurfer] GONE: -make to recon-all > >     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> > >     Message-ID:<9DB20083-D647-47E0-9396-C24308B503B9(a)uiowa.edu>  <mailto:9DB20083-D647-47E0-9396-C24308B503B9@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/202007… > >     ------------------------------ > >     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>  <mailto:ladn@email.gwu.edu> > >     Subject: Re: [Freesurfer] fsgd file - glmfit error > >     To: Freesurfer support list<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID: > >              <CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA(a)mail.gmail.com>  <mailto:CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA@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>  <mailto:dgreve@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>  <mailto:dgreve@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  <mailto:listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma> > >             ilman/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 > >         listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai  <mailto:listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai> > >         lman/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 > >     -------------- next part -------------- > >     An HTML attachment was scrubbed... > >     URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/202007… > >     ------------------------------ > >     Message: 6 > >     Date: Thu, 30 Jul 2020 09:34:12 +0000 > >     From: "Zollei, Lilla,Ph.D."<LZOLLEI(a)mgh.harvard.edu>  <mailto:LZOLLEI@mgh.harvard.edu> > >     Subject: Re: [Freesurfer] Recon-all Soft Errors > >     To: Freesurfer support list<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID: > >              <DM6PR04MB44127C2DB157BB07AB669F41E3710(a)DM6PR04MB4412.namprd04.prod.outlook.com>  <mailto:DM6PR04MB44127C2DB157BB07AB669F41E3710@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@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 Elana Sarabin<elana.sarabin1(a)ucalgary.ca>  <mailto:elana.sarabin1@ucalgary.ca> > >     Sent: Wednesday, July 29, 2020 11:02 AM > >     To: Freesurfer support list<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@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/202007… > >     ------------------------------ > >     Message: 7 > >     Date: Thu, 30 Jul 2020 17:49:49 +0430 > >     From: Hengameh Marzbani<marzbani91(a)gmail.com>  <mailto:marzbani91@gmail.com> > >     Subject: [Freesurfer] bad interpreter: No such file or directory error > >     To: Freesurfer support list<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID: > >              <CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw(a)mail.gmail.com>  <mailto:CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw@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/202007… > >     ------------------------------ > >     Message: 8 > >     Date: Thu, 30 Jul 2020 10:20:07 -0400 > >     From: "Douglas N. Greve"<dgreve(a)mgh.harvard.edu>  <mailto:dgreve@mgh.harvard.edu> > >     Subject: Re: [Freesurfer] overlapping/ superimposing regions of one > >      ??????? analysis over another > >     To:<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID:<c4e336e0-b3b8-89eb-e59b-1894fdf856b8(a)mgh.harvard.edu>  <mailto:c4e336e0-b3b8-89eb-e59b-1894fdf856b8@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>  <mailto:khokharsunil1@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>  <mailto:dgreve@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>  <mailto:khokharsunil1@gmail.com>  <mailto:khokharsunil1@gmail.com> > >              ??? +91-9413101839 > >              ??? _______________________________________________ > >              ??? 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/mailman/listinfo/freesurfer > >          ??? _______________________________________________ > >          ??? 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/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 > >     -------------- next part -------------- > >     An HTML attachment was scrubbed... > >     URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/202007… > >     ------------------------------ > >     Message: 9 > >     Date: Thu, 30 Jul 2020 10:21:14 -0400 > >     From: "Douglas N. Greve"<dgreve(a)mgh.harvard.edu>  <mailto:dgreve@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>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID:<ec2eef74-6cd8-0c36-dbeb-983240090223(a)mgh.harvard.edu>  <mailto:ec2eef74-6cd8-0c36-dbeb-983240090223@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  <mailto:Freesurfer@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/202007… > >     ------------------------------ > >     Message: 10 > >     Date: Thu, 30 Jul 2020 10:26:22 -0400 > >     From: "Douglas N. Greve"<dgreve(a)mgh.harvard.edu>  <mailto:dgreve@mgh.harvard.edu> > >     Subject: Re: [Freesurfer] Recon-all Soft Errors > >     To:<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID:<78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8(a)mgh.harvard.edu>  <mailto:78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8@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  <mailto:Freesurfer@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/202007… > >     ------------------------------ > >     Message: 11 > >     Date: Thu, 30 Jul 2020 11:31:47 -0400 > >     From: "Douglas N. Greve"<dgreve(a)mgh.harvard.edu>  <mailto:dgreve@mgh.harvard.edu> > >     Subject: Re: [Freesurfer] Coregistration to MNI > >     To: "Camargo, Aldo"<ACamargo(a)som.umaryland.edu>  <mailto:ACamargo@som.umaryland.edu>, Freesurfer support > >      ??????? list<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID:<9af8c73e-46a8-e9b6-4b84-ce507589efed(a)mgh.harvard.edu>  <mailto:9af8c73e-46a8-e9b6-4b84-ce507589efed@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>  <mailto:dgreve@mgh.harvard.edu> > >         *Sent:* Wednesday, July 29, 2020 10:39 AM > >         *To:* Camargo, Aldo<ACamargo(a)som.umaryland.edu>  <mailto:ACamargo@som.umaryland.edu>; Freesurfer support > >         list<freesurfer(a)nmr.mgh.harvard.edu>  <mailto:freesurfer@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>  > >             <mailto:ACamargo@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>  > >             <mailto:dgreve@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@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 Douglas > >             N. Greve<dgreve(a)mgh.harvard.edu>  <mailto:dgreve@mgh.harvard.edu>  <mailto:dgreve@mgh.harvard.edu>  <mailto:dgreve@mgh.harvard.edu> > >             *Sent:* Monday, July 27, 2020 10:46 AM > >             *To:*freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >             <mailto:freesurfer@nmr.mgh.harvard.edu>  <mailto:freesurfer@nmr.mgh.harvard.edu> > >             <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] 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@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 > >                 Camargo, Aldo<ACamargo(a)som.umaryland.edu>  <mailto:ACamargo@som.umaryland.edu>  > >                 <mailto:ACamargo@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>  > >                 <mailto:freesurfer@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> > >                 <mailto:Freesurfer@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 athttp://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/202007… > >     ------------------------------ > >     Message: 12 > >     Date: Thu, 30 Jul 2020 17:39:06 +0200 > >     From: Ellen Ji<ellen.ji(a)bli.uzh.ch>  <mailto:ellen.ji@bli.uzh.ch> > >     Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output > >      ??????? labels? > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Message-ID:<24cc8874-81ee-1e68-85ad-b8fe662c4fc3(a)bli.uzh.ch>  <mailto:24cc8874-81ee-1e68-85ad-b8fe662c4fc3@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  <mailto:ellen.ji@bli.uzh.ch> > >     homanlab.github.io/ellen/ > >     ------------------------------ > >     Message: 13 > >     Date: Thu, 30 Jul 2020 17:48:25 +0200 > >     From: fsbuild<fsbuild(a)contbay.com>  <mailto:fsbuild@contbay.com> > >     Subject: Re: [Freesurfer] bad interpreter: No such file or directory > >      ??????? error > >     To:freesurfer@nmr.mgh.harvard.edu  <mailto:freesurfer@nmr.mgh.harvard.edu> > >     Cc:marzbani91@gmail.com  <mailto:marzbani91@gmail.com> > >     Message-ID:<1596124105.5f22ebc98f04a(a)trashmail.com>  <mailto:1596124105.5f22ebc98f04a@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, > >     $&nbsp;sudo&nbsp;apt-get install csh tcsh > >     - R.. > >     On Jul 30, 2020, at 09:19, Hengameh Marzbani &lt;marzbani91(a)gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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&nbsp;The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, Hengameh_______________________________________________Freesurfer mailinglistFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <mailto: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/202007… > >     ------------------------------ > >     _______________________________________________ > >     Freesurfer mailing list > >     Freesurfer(a)nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu> > >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >     End of Freesurfer Digest, Vol 197, Issue 59 > >     ******************************************* > > > >     _______________________________________________ > >     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/20200807/9… ------------------------------ Message: 4 Date: Fri, 7 Aug 2020 10:18:40 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_vol2vol and diffusion issue To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <a16871a9-4604-3a8c-cfcd-b83e9a1ff30b(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" What version of FS are you using? Can you send the log? file? On 8/6/2020 6:55 AM, ? ? wrote: > > ????????External Email - Use Caution > > Hello! freesurfer experts, > I am running dt_recon and mri_vol2vol to obtain FA values of five > corpus callosum (CC) sub-regions. > > command1, dt_recon --b bvals.dat bvecs.dat --i > $TUTORIAL_DIR/$subj/DTI/00001.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon > > ?command 2, mri_vol2vol --mov lowb.nii.gz \ > > --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ > > --inv --interp nearest --o $SUB?JECTS_DIR/$subj/mri/wmparc2diff.mgz \ > > --reg register.dat --no-save-reg > > ? Everything is OK after running the dt_recon command and the > registration of all diffusion images with the anatomical data is good. > However, some of my subjects show an issue with mri_vol2vol > registration. When checking the wmparc2diff.mgz I created, it is > apparent tha?t surfaces of lh.white and rh.white are not accurately > mismatched with the wmparc2diff.mgz, as showed in the following > figure. Is there an error with my command about mri_vol2vol or a > problem in other aspects? ? ?Any advice with troubleshooting would be > greatly appreciated.? Best Wishes ? Bo Tao M.D Student, Department of > Radiology / Huaxi MR Research Center (HMRRC?West China Hospital of > Sichuan University Chengdu? City, 610041? P.R. China? > ?? ?? > > > _______________________________________________ > 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/20200807/c… -------------- next part -------------- A non-text attachment was scrubbed... Name: 58073AFE(a)6751A60F.9FE12B5F.png.jpg Type: image/jpeg Size: 404700 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200807/c… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 198, Issue 11 ******************************************* 从QQ邮箱发来的超大附件 ST_LS_094.tar.gz (642.83M, 2020年09月09日 15:43 到期)进入下载页面：http://mail.qq.com/cgi-bin/ftnExs_download?t=exs_ftn_download&k=2…

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Mean curvature comparison
by Avi Gharehgazlou 10 Aug '20

10 Aug '20

External Email - Use Caution Hi, I want to compare mean curvature between groups on QDEC using the “curv” measure. I've learned from the archives that FreeSurfer calculates numerous curvature-based functions by default in the recon stream and stores them in the “surf” directory. I have 3 questions that I would appreciate your advice on: 1. I’ve already ran recon-all on all my subjects. Then, I also ran the below command line for qcache. The "-measure lgi" is in my command line because I am also planning to look at lGI differences between groups and this is the qcache command line I use for the lGI measure. Now I'm asking if this command line is appropriate for me to proceed with comparing mean curvature between groups as well? or should I run a different qcache command line before starting statistical analyses on mean curvature? recon-all -s PC03_01 -qcache -measure pial_lgi 2. I don't smooth the lGI measure as the computation of this measure makes it a relatively smooth construct. However, for mean curvature: what level of smoothing do you recommend (i.e. 10 FWHM)? 3. I control for surface area when comparing lGI values between groups. However, for mean curvature group comparisons, should I be controlling for intracranial volume (ICV) instead? I'd really appreciate your advice, Thank you so much, Avi

1 0

Skull strip t1 in recon-all
by Julie Ottoy 10 Aug '20

10 Aug '20

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz ./FreeSurfer/ID/mri/brainmask.mgz 3) run recon-all with -autorecon-2 and autorecon-3 My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore, when transforming to the size of brainmask.mgz (256x256x256), it deforms. I tried nearest, cubic, and interpolate, but none of them gives actually a good result in terms of retaining the contrast. I was wondering if it is important to keep a good contrast for brainmask.mgz , or whether this brainmask.mgz is just used to determine the brain borders for segmentation. (ie.: in which steps of recon-all is the brainmask.mgz actually used and for what?) Any recommendations? Thank you!

1 0

cortical surface area calculation
by Alexopoulos, Dimitrios 10 Aug '20

10 Aug '20

External Email - Use Caution Hi all, Does this command calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats 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.

2 1

Hippocampus_substructures_normalization
by Haewon Roh 10 Aug '20

10 Aug '20

External Email - Use Caution Hi. team! Recently, I submitted a paper dealing with volumes of hippocampus and its subfields in epilepsy patients who have significantly reduced hippocampal volume (compared with normal controls) and, in that paper, I used the normalization method using ICV, which was suggested by Jack CR in 1989: normalized volume = volume (observed) – b (ICV – mean ICV), where b is the slope of regression for each ICV. But, one of the reviewers pointed out that I should use the method based on each patient's hippocampus rather than total intracranial volume. Since I've seen that a lot of papers, which dealt about these kinds of issues about hippocampus and subfields, used the same method with me, I am really doubtful that it is more appropriate if I should use the method using individual volume of hippocampus (rather than ICV) in order to normalize its volumes of substructures in the comparison analysis with those of controls. # And, whether this is true or not, could you please recommend to me several literatures that can show which method of normalizing volumes of the hippocampus and its subfields is more appropriate for this kind of issue? # Really sorry for bothering you. Thank you always for your kind and delicate solutions ! : ) -- Hae Won ROH, M.D. H.P: +82-10-4341-8142 E-mail: rofree1st(a)gmail.com

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Directories not populating after recon-all
by Rohin Singh 08 Aug '20

08 Aug '20

External Email - Use Caution Hello, I am a student at the Mayo Clinic trying to do a project with fresurfer. When I run recon-all, it only creates one file “001.mgz” in the MRI directory and the rest of the folders are blank. I am not sure why this is as it completes the process without any errors and I followed the set up instructions exactly. Any help would be greatly appreciated. Thanks, Rohin Singh

2 1

Question regarding Euler number
by Scheffler, F, Mev [fredas＠sun.ac.za] 07 Aug '20

07 Aug '20

External Email - Use Caution Dear FreeSurfer Devs I got a comment about including a SNR variable in my main stats analysis and so came across a Rosen et al 2018 paper which refers to the Euler number. I then checked the archives and came across a thread<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58748.html> where you say that in version 6.0 the numbers are included in the aseg.stats file, specifically as a global measure called SurfaceHoles. With regards to our QC procedures: We visually inspected all of our scans and then followed ENIGMA’s quality assessment protocols. We excluded scans with motion artefacts or poor-quality images and only included the data from the scans with acceptable or good quality segmentation. Outlier detection and the distribution of our data was also checked prior to analysis of the data. So, my question is, can I include the SurfaceHoles variable in my model as a proxy for SNR? Would that be sensible, or do you have an alternative suggestion? Thanks very much! Kind regards, Freda Scheffler PhD Candidate

3 2

LGI and Global GI
by Alexopoulos, Dimitrios 07 Aug '20

07 Aug '20

External Email - Use Caution HI, I have generated the LGI for a group of pediatric subjects. Is there a way to compute a single Global gyrification index measure for each subject? 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.

2 3

labels in .nii file
by Eleni Nikalexi 07 Aug '20

07 Aug '20

External Email - Use Caution Dear Freesurfer developers,We have a volume that assigns unique numerical labels to each of the ROIs it contains, in NIFTI format. I want to register it to MNI152 (1mm) space, so that I can map it on my subjects and use mris_anatomical_stats.I have tried the following command: 1. tkregisterfv --mov MDROI.nii --s MNI_1mm --regheader --reg registrationMD/MDROI.lta to get : "LTA input is not RAS to RAS...converting...". Then I run: 2. mri_vol2surf --src MDROI.nii --src_type nii --out registrationMD/surf.MDROI.mgh --reg registrationMD/MDROI.lta --hemi lh --surf white --projdist-max 0 1 0.1 3. mri_vol2surf --src MDROI.nii --src_type nii --out registrationMD/surf.MDROI_rh.mgh --reg registrationMD/MDROI.lta --hemi rh --surf white --projdist-max 0 1 0.1The 2 commands above demand the --hemi argument, but I wasn't sure what to put, as the ROIs are mixed and are in both hemispheres. Thus I run the command once for the left and once for the right hemisphere, creating different .mgh files.Last, I continued with: 4. mri_vol2label --i registrationMD/surf.MDROI.mgh --id 1 --l lab.MDROI_lh.label --surf MNI_1mm l which failed, as I get "ERROR: found no voxels matching id 1" Could you please tell me, if the commands make sense, and if I should change something? Thank you so much for your help! Best regards,Eleni

2 3

mri_vol2vol and diffusion issue
by 真我 07 Aug '20

07 Aug '20

External Email - Use Caution Hello! freesurfer experts,I am running dt_recon and mri_vol2vol to obtain FA values of five corpus callosum (CC) sub-regions. command 1, dt_recon --b bvals.dat bvecs.dat --i $TUTORIAL_DIR/$subj/DTI/00001.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon command 2, mri_vol2vol --mov lowb.nii.gz \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --reg register.dat --no-save-reg Everything is OK after running the dt_recon command and the registration of all diffusion images with the anatomical data is good. However, some of my subjects 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 accurately mismatched with the wmparc2diff.mgz, as showed in the following figure. Is there an error with my command about mri_vol2vol or a problem in other aspects? Any advice with troubleshooting would be greatly appreciated. Best Wishes Bo Tao M.D Student, Department of Radiology / Huaxi MR Research Center (HMRRC）West China Hospital of Sichuan University Chengdu  City, 610041 P.R. China

2 1

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