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@nmr.mgh.harvard.edu&gt;; Date:&nbsp;Fri, Aug 7, 2020 10:18 PM To:&nbsp;"freesurfer"<freesurfer@nmr.mgh.harvard.edu&gt;;

Subject:&nbsp;Freesurfer Digest, Vol 198, Issue 11

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Today's Topics:

&nbsp;&nbsp; 1. Re: labels in .nii file (Douglas N. Greve) &nbsp;&nbsp; 2. Re: high pass filter cutoff (Douglas N. Greve) &nbsp;&nbsp; 3. Re: Recon-all Soft Errors (Douglas N. Greve) &nbsp;&nbsp; 4. Re: mri_vol2vol and diffusion issue (Douglas N. Greve)

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Message: 1 Date: Fri, 7 Aug 2020 10:10:43 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu&gt; Subject: Re: [Freesurfer] labels in .nii file To: <freesurfer@nmr.mgh.harvard.edu&gt; Message-ID: <95d0a55e-80c2-915c-caf3-e45af6c8a9c1@mgh.harvard.edu&gt; 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: &gt; &gt; ????????External Email - Use Caution &gt; &gt; Dear Freesurfer developers, &gt; We have a volume that assigns unique numerical labels to each of the &gt; ROIs it contains, in NIFTI format. I want to register it to MNI152 &gt; (1mm) space, so that I can map it on my subjects and use &gt; mris_anatomical_stats. &gt; I have tried the following command: &gt; &gt; 1. tkregisterfv --mov MDROI.nii --s MNI_1mm --regheader --reg &gt; registrationMD/MDROI.lta &gt; &gt; to get : ?"LTA input is not RAS to RAS...converting...". &gt; Then I run: &gt; &gt; ????????2. mri_vol2surf --src MDROI.nii --src_type nii --out &gt; registrationMD/surf.MDROI.mgh --reg &gt; ????????????registrationMD/MDROI.lta --hemi lh?--surf white &gt; --projdist-max 0 1 0.1 &gt; ? ? ?3. mri_vol2surf --src MDROI.nii --src_type nii --out &gt; registrationMD/surf.MDROI_rh.mgh --reg &gt; ????????????registrationMD/MDROI.lta --hemi rh?--surf white &gt; --projdist-max 0 1 0.1 &gt; The 2 commands above demand the --hemi argument, but I wasn't sure &gt; what to put, as the ROIs are mixed and are in both hemispheres. Thus I &gt; run the command once for the left and once for the right hemisphere, &gt; creating different .mgh files. &gt; Last, I continued with: &gt; &gt; ? ? ? ? 4. mri_vol2label --i registrationMD/surf.MDROI.mgh --id 1 --l &gt; lab.MDROI_lh.label --surf MNI_1mm l &gt; &gt; which failed, as I get "ERROR: found no voxels matching id 1" &gt; &gt; Could you please tell me, if the commands make sense, and if I should &gt; change something? &gt; &gt; Thank you so much for your help! &gt; &gt; Best regards, &gt; Eleni &gt; &gt; _______________________________________________ &gt; Freesurfer mailing list &gt; Freesurfer@nmr.mgh.harvard.edu &gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 2 Date: Fri, 7 Aug 2020 10:15:01 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu&gt; Subject: Re: [Freesurfer] high pass filter cutoff To: <freesurfer@nmr.mgh.harvard.edu&gt; Message-ID: <d1c723ac-8baa-af79-5812-fcffae6eaacb@mgh.harvard.edu&gt; 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: &gt; Hi Freesurferers &gt; &gt; 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)? &gt; 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. &gt; I have used a hpf=0.01, Is this correct? &gt; &gt; Thanks &gt; Mona &gt; &gt; &gt; _______________________________________________ &gt; Freesurfer mailing list &gt; Freesurfer@nmr.mgh.harvard.edu &gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 3 Date: Fri, 7 Aug 2020 10:17:42 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu&gt; Subject: Re: [Freesurfer] Recon-all Soft Errors To: <freesurfer@nmr.mgh.harvard.edu&gt; Message-ID: <80109940-d6ff-33f5-faff-d836725e829b@mgh.harvard.edu&gt; 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: &gt; &gt; ????????External Email - Use Caution &gt; &gt; Here is one photo. Seems this is the most I can send at once. Most &gt; errors look just like this however sometimes larger and sometimes smaller. &gt; &gt; Best, &gt; &gt; Elana &gt; &gt; *From: *<freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of "Douglas &gt; N. Greve" <dgreve@mgh.harvard.edu&gt; &gt; *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu&gt; &gt; *Date: *Tuesday, August 4, 2020 at 8:01 AM &gt; *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu&gt; &gt; *Subject: *Re: [Freesurfer] Recon-all Soft Errors &gt; &gt; [?EXTERNAL] &gt; &gt; Can you send a picture of the type of errors you are seeing? &gt; &gt; On 7/31/2020 9:03 AM, Elana Sarabin wrote: &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Here is the recon-all.log file. &gt; &gt;&nbsp;&nbsp; &nbsp; Thanks, &gt; &gt;&nbsp;&nbsp; &nbsp; Elana &gt; &gt;&nbsp;&nbsp; &nbsp; -----Original Message----- &gt; &gt;&nbsp;&nbsp; &nbsp; From: Elana Sarabin &gt; &gt;&nbsp;&nbsp; &nbsp; Sent: July 30, 2020 10:21 AM &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: Recon-all Soft Errors &gt; &gt;&nbsp;&nbsp; &nbsp; Here is the recon-all.log file. &gt; &gt;&nbsp;&nbsp; &nbsp; Thanks, &gt; &gt;&nbsp;&nbsp; &nbsp; Elana &gt; &gt;&nbsp;&nbsp; &nbsp; -----Original Message----- &gt; &gt;&nbsp;&nbsp; &nbsp; From:freesurfer-bounces@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; On Behalf Offreesurfer-request@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-request@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Sent: July 30, 2020 10:00 AM &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Freesurfer Digest, Vol 197, Issue 59 &gt; &gt;&nbsp;&nbsp; &nbsp; [?EXTERNAL] &gt; &gt;&nbsp;&nbsp; &nbsp; Send Freesurfer mailing list submissions to &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; To subscribe or unsubscribe via the World Wide Web, visit &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp; &nbsp; or, via email, send a message with subject or body 'help' to &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; freesurfer-request@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-request@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; You can reach the person managing the list at &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; freesurfer-owner@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-owner@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." &gt; &gt;&nbsp;&nbsp; &nbsp; Today's Topics: &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 1. FS 7.1.0 - Editing intensity values for WM (Nils B?er) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 3. Creating .annot file for a mri_decimate downsampeld?????? version &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ????? of pial surface (Donelson Berger) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 4. GONE: -make to recon-all (Johnson, Hans J) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 5. Re: fsgd file - glmfit error &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ????? (Lab of Autism and Developmental Neuroscience,??? Lab of Autism and Developmental Neuroscience) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 7. bad interpreter: No such file or directory error &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ????? (Hengameh Marzbani) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 8. Re: overlapping/ superimposing regions of one analysis over &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ????? another (Douglas N. Greve) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ?? 9. Re: Creating .annot file for a mri_decimate downsampeld &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ????? version of pial surface (Douglas N. Greve) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ? 10. Re: Recon-all Soft Errors (Douglas N. Greve) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ? 11. Re: Coregistration to MNI (Douglas N. Greve) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ? 12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji) &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ? 13. Re: bad interpreter: No such file or directory error (fsbuild) &gt; &gt;&nbsp;&nbsp; &nbsp; ---------------------------------------------------------------------- &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 1 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Wed, 29 Jul 2020 21:27:03 +0200 &gt; &gt;&nbsp;&nbsp; &nbsp; From: Nils B?er<nils.tobias94@gmail.com&gt;&nbsp; <mailto:nils.tobias94@gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw@mail.gmail.com&gt;&nbsp; <mailto:CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw@mail.gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Hello everyone, &gt; &gt;&nbsp;&nbsp; &nbsp; I just have a short question, because I can't find anything helpful in the tutorials. &gt; &gt;&nbsp;&nbsp; &nbsp; 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. &gt; &gt;&nbsp;&nbsp; &nbsp; I'd be thankful for any feedback/links to guides. &gt; &gt;&nbsp;&nbsp; &nbsp; Best regards, &gt; &gt;&nbsp;&nbsp; &nbsp; Nils &gt; &gt;&nbsp;&nbsp; &nbsp; -- &gt; &gt;&nbsp;&nbsp; &nbsp; Nils B?er &gt; &gt;&nbsp;&nbsp; &nbsp; Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 &gt; &gt;&nbsp;&nbsp; &nbsp; 33098 Paderborn &gt; &gt;&nbsp;&nbsp; &nbsp; Room: Sp 1.401 &gt; &gt;&nbsp;&nbsp; &nbsp; Email:nils.tobias94@gmail.com&nbsp; <mailto:nils.tobias94@gmail.com&gt;&nbsp; /nboeer@mail.uni-paderborn.de&nbsp; <mailto:nboeer@mail.uni-paderborn.de&gt;&nbsp; <nils.tobias94@gmail.com&gt;&nbsp; <mailto:nils.tobias94@gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Web:https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://sug.uni-paderborn.de/department/it/ &gt; &gt;&nbsp;&nbsp; &nbsp; <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/%3E%C2%A0; <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/%3E; &gt; &gt;&nbsp;&nbsp; &nbsp; <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; &gt; &gt;&nbsp;&nbsp; &nbsp; Virenfrei. &gt; &gt;&nbsp;&nbsp; &nbsp; www.avast.com&nbsp; <http://www.avast.com%3E; &gt; &gt;&nbsp;&nbsp; &nbsp; <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; &gt; &gt;&nbsp;&nbsp; &nbsp; <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/45... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 2 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Wed, 29 Jul 2020 20:32:34 +0000 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Fischl, Bruce"<BFISCHL@mgh.harvard.edu&gt;&nbsp; <mailto:BFISCHL@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM &gt; &gt;&nbsp;&nbsp; &nbsp; To:"freesurfer@nmr.mgh.harvard.edu"&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <BL0PR04MB660985EC505DEECB596362ADEF700@BL0PR04MB6609.namprd04.prod.outlook.com&gt;&nbsp; <mailto:BL0PR04MB660985EC505DEECB596362ADEF700@BL0PR04MB6609.namprd04.prod.outlook.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp; &nbsp; Hi Nils &gt; &gt;&nbsp;&nbsp; &nbsp; 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 &gt; &gt;&nbsp;&nbsp; &nbsp; Cheers &gt; &gt;&nbsp;&nbsp; &nbsp; Bruce &gt; &gt;&nbsp;&nbsp; &nbsp; From:freesurfer-bounces@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; On Behalf Of Nils B?er &gt; &gt;&nbsp;&nbsp; &nbsp; Sent: Wednesday, July 29, 2020 3:27 PM &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Hello everyone, &gt; &gt;&nbsp;&nbsp; &nbsp; I just have a short question, because I can't find anything helpful in the tutorials. &gt; &gt;&nbsp;&nbsp; &nbsp; 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. &gt; &gt;&nbsp;&nbsp; &nbsp; I'd be thankful for any feedback/links to guides. &gt; &gt;&nbsp;&nbsp; &nbsp; Best regards, &gt; &gt;&nbsp;&nbsp; &nbsp; Nils &gt; &gt;&nbsp;&nbsp; &nbsp; -- &gt; &gt;&nbsp;&nbsp; &nbsp; Nils B?er &gt; &gt;&nbsp;&nbsp; &nbsp; Research Assistant with Bachelor Degree (WHB) Psychology and Movement University of Paderborn Department of Sports and Health Warburger Str. 100 &gt; &gt;&nbsp;&nbsp; &nbsp; 33098 Paderborn &gt; &gt;&nbsp;&nbsp; &nbsp; Room: Sp 1.401 &gt; &gt;&nbsp;&nbsp; &nbsp; Email:nils.tobias94@gmail.com&nbsp; <mailto:nils.tobias94@gmail.com&gt;&nbsp; /nboeer@mail.uni-paderborn.de&nbsp; <mailto:nboeer@mail.uni-paderborn.de&gt;<mailto:nils.tobias94@gmail.com&gt;&nbsp; <mailto:nils.tobias94@gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Web:https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://sug.uni-paderborn.de/department/it/<https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/%3E%C2%A0; <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/%3E; &gt; &gt;&nbsp;&nbsp; &nbsp; [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animat...]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; &gt; &gt;&nbsp;&nbsp; &nbsp; Virenfrei.www.avast.com&nbsp; <http://www.avast.com%3E;<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm...; &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/a4... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 3 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Wed, 29 Jul 2020 15:51:03 -0500 &gt; &gt;&nbsp;&nbsp; &nbsp; From: Donelson Berger<donelsongrahamberger@gmail.com&gt;&nbsp; <mailto:donelsongrahamberger@gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] Creating .annot file for a mri_decimate &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? downsampeld???? version of pial surface &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA@mail.gmail.com&gt;&nbsp; <mailto:CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA@mail.gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Hello FreeSurfer Expert, &gt; &gt;&nbsp;&nbsp; &nbsp; 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. &gt; &gt;&nbsp;&nbsp; &nbsp; 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. &gt; &gt;&nbsp;&nbsp; &nbsp; Do you have any suggestions? &gt; &gt;&nbsp;&nbsp; &nbsp; Thanks for your help, &gt; &gt;&nbsp;&nbsp; &nbsp; Donelson Graham Berger &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/d8... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 4 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Wed, 29 Jul 2020 22:22:47 +0000 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Johnson, Hans J"<hans-johnson@uiowa.edu&gt;&nbsp; <mailto:hans-johnson@uiowa.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] GONE: -make to recon-all &gt; &gt;&nbsp;&nbsp; &nbsp; To:"freesurfer@nmr.mgh.harvard.edu"&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<9DB20083-D647-47E0-9396-C24308B503B9@uiowa.edu&gt;&nbsp; <mailto:9DB20083-D647-47E0-9396-C24308B503B9@uiowa.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; 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. &gt; &gt;&nbsp;&nbsp; &nbsp; 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 &gt; &gt;&nbsp;&nbsp; &nbsp; Q1)? should "recon-all -make all" be avoided for FreeSurfer 7.1.0? &gt; &gt;&nbsp;&nbsp; &nbsp; Q2) is there an alternate way to "continue form the point where results are missing" in the pipeline? &gt; &gt;&nbsp;&nbsp; &nbsp; Thanks, &gt; &gt;&nbsp;&nbsp; &nbsp; Hans &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/f7... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 5 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Wed, 29 Jul 2020 15:49:44 -0700 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Lab of Autism and Developmental Neuroscience,??? Lab of Autism and &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? Developmental Neuroscience"<ladn@email.gwu.edu&gt;&nbsp; <mailto:ladn@email.gwu.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] fsgd file - glmfit error &gt; &gt;&nbsp;&nbsp; &nbsp; To: Freesurfer support list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA@mail.gmail.com&gt;&nbsp; <mailto:CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA@mail.gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Thank you Douglas! &gt; &gt;&nbsp;&nbsp; &nbsp; On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Try putting 1 after GroupDescriptorFile, ie, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; GroupDescriptorFile 1 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Lab of Autism and Developmental Neuroscience wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Here is my fsgd file. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Thank you! &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Please send the fsgd file &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Lab of Autism and Developmental Neuroscience wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Dear Freesurfer experts, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hope this email finds you well. I am having some trouble with the &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; fsgd file for glmfit and I'm confused why. This is the error I'm &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; getting when running glmfit: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; gdfRead(): reading fsgd_8.fsgd &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; iMac-Pro:BAP_complete ajobsaid$ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; If needed, I can send you my fsgd file, but I have triple checked the &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; design and format of the file (it is saved as .fsgd), and I'm still &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; getting this error message. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Thank you, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Alex &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma%C2%A0; <mailto:listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/ma%3E; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ilman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai%C2%A0; <mailto:listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai%3E; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; lman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200729/24... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 6 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 09:34:12 +0000 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Zollei, Lilla,Ph.D."<LZOLLEI@mgh.harvard.edu&gt;&nbsp; <mailto:LZOLLEI@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] Recon-all Soft Errors &gt; &gt;&nbsp;&nbsp; &nbsp; To: Freesurfer support list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <DM6PR04MB44127C2DB157BB07AB669F41E3710@DM6PR04MB4412.namprd04.prod.outlook.com&gt;&nbsp; <mailto:DM6PR04MB44127C2DB157BB07AB669F41E3710@DM6PR04MB4412.namprd04.prod.outlook.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="windows-1252" &gt; &gt;&nbsp;&nbsp; &nbsp; Hi Elena, &gt; &gt;&nbsp;&nbsp; &nbsp; What is the age range of your subjects? &gt; &gt;&nbsp;&nbsp; &nbsp; Best, Lilla &gt; &gt;&nbsp;&nbsp; &nbsp; ________________________________ &gt; &gt;&nbsp;&nbsp; &nbsp; From:freesurfer-bounces@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; on behalf of Elana Sarabin<elana.sarabin1@ucalgary.ca&gt;&nbsp; <mailto:elana.sarabin1@ucalgary.ca&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Sent: Wednesday, July 29, 2020 11:02 AM &gt; &gt;&nbsp;&nbsp; &nbsp; To: Freesurfer support list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] Recon-all Soft Errors &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Hi Freesurfer experts, &gt; &gt;&nbsp;&nbsp; &nbsp; 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. &gt; &gt;&nbsp;&nbsp; &nbsp; Thanks, &gt; &gt;&nbsp;&nbsp; &nbsp; Elana &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/dc... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 7 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 17:49:49 +0430 &gt; &gt;&nbsp;&nbsp; &nbsp; From: Hengameh Marzbani<marzbani91@gmail.com&gt;&nbsp; <mailto:marzbani91@gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] bad interpreter: No such file or directory error &gt; &gt;&nbsp;&nbsp; &nbsp; To: Freesurfer support list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw@mail.gmail.com&gt;&nbsp; <mailto:CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw@mail.gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Hello Freesurfer developers, &gt; &gt;&nbsp;&nbsp; &nbsp; I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. &gt; &gt;&nbsp;&nbsp; &nbsp; Also, freeview works by simply typing the freeview command. &gt; &gt;&nbsp;&nbsp; &nbsp; However,I have tried to run recon-all. but, I have got the following error message on all PCs: &gt; &gt;&nbsp;&nbsp; &nbsp; *bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory* &gt; &gt;&nbsp;&nbsp; &nbsp; also The build-stamps.txt file contents: &gt; &gt;&nbsp;&nbsp; &nbsp; *freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b* &gt; &gt;&nbsp;&nbsp; &nbsp; Thank you in advance, &gt; &gt;&nbsp;&nbsp; &nbsp; Best regards, &gt; &gt;&nbsp;&nbsp; &nbsp; Hengameh &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/48... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 8 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 10:20:07 -0400 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Douglas N. Greve"<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] overlapping/ superimposing regions of one &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? analysis over another &gt; &gt;&nbsp;&nbsp; &nbsp; To:<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<c4e336e0-b3b8-89eb-e59b-1894fdf856b8@mgh.harvard.edu&gt;&nbsp; <mailto:c4e336e0-b3b8-89eb-e59b-1894fdf856b8@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp; &nbsp; 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 &gt; &gt;&nbsp;&nbsp; &nbsp; On 7/27/2020 2:17 PM, Sunil Khokhar wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; To operate the visualization and obtain the common regions of my &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; between-group difference results and the correlation results in one &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; image. In other?words, overlapping/ superimposing?my correlation &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; results on the between-group results (to obtain the common regions &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; from the two separate analysis). &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Thanks &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Sunil K Khokhar &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; PhD Scholar, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Department of Neuroimaging &amp; Interventional Radiology, NIMHANS, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Bengaluru, INDIA. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; khokharsunil1@gmail.com&nbsp; <mailto:khokharsunil1@gmail.com&gt;&nbsp; <mailto:khokharsunil1@gmail.com&gt;&nbsp; <mailto:khokharsunil1@gmail.com&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; +91-9413101839 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; On Mon, Jul 27, 2020 at 8:21 PM Douglas N. Greve &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <dgreve@mgh.harvard.edu&nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&gt; wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? are you asking how to create positive and negative regions or are &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? you asking how to operate the visualization? &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? On 7/25/2020 9:40 AM, Sunil Khokhar wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Dear Experts, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? I have done a between group (2 groups) difference in whole brain &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? voxel based cortical thickness using QDEC, which showed &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? significant regional differences in certain clusters &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? bilaterally?in the brain. I also did a correlation between &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? cortical thickness and behavioral scores separately?in these two &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? groups. Now, I want to superimpose regions (clusters) which &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? showed positive and negative correlation on the?results/ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? regions?I obtained in my between group analysis. How can I do this? &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Thanks in advance! &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Sunil. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? _______________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Sunil K Khokhar &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? PhD Scholar, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Department of Neuroimaging &amp; Interventional Radiology, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? NIMHANS, Bengaluru, INDIA. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; khokharsunil1@gmail.com&nbsp; <mailto:khokharsunil1@gmail.com&gt;&nbsp; <mailto:khokharsunil1@gmail.com&gt;&nbsp; <mailto:khokharsunil1@gmail.com&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? +91-9413101839 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??? Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/7d... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 9 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 10:21:14 -0400 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Douglas N. Greve"<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] Creating .annot file for a mri_decimate &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? downsampeld version of pial surface &gt; &gt;&nbsp;&nbsp; &nbsp; To:<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<ec2eef74-6cd8-0c36-dbeb-983240090223@mgh.harvard.edu&gt;&nbsp; <mailto:ec2eef74-6cd8-0c36-dbeb-983240090223@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp; &nbsp; Use &gt; &gt;&nbsp;&nbsp; &nbsp; mris_apply_reg --sval-annot lh.your.annot --streg lh.pial lh.pial.decimated --o lh.your.decimated.annot &gt; &gt;&nbsp;&nbsp; &nbsp; On 7/29/2020 4:51 PM, Donelson Berger wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hello FreeSurfer Expert, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I've run into a problem that I just can't seem to solve. After &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; and 10,002 points, I don't know how to create .annot files for the new &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; surfaces I created. I want to be able to tell which ROI each vertex is &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; in for my new surface based off a parcellation. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I've been trying to use mri_ca_label, mri_ca_train, and &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; mris_sample_parc, but I can't seem to get anything to work. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Do you have any suggestions? &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Thanks for your help, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Donelson Graham Berger &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/e6... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 10 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 10:26:22 -0400 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Douglas N. Greve"<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] Recon-all Soft Errors &gt; &gt;&nbsp;&nbsp; &nbsp; To:<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8@mgh.harvard.edu&gt;&nbsp; <mailto:78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="windows-1252" &gt; &gt;&nbsp;&nbsp; &nbsp; for the first error, can you send the recon-all.log file? &gt; &gt;&nbsp;&nbsp; &nbsp; For the second error, you need to adjust the intensity ranges. For some reason they are coming up as 0s. &gt; &gt;&nbsp;&nbsp; &nbsp; On 7/29/2020 11:02 AM, Elana Sarabin wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hi Freesurfer experts, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I am a first time user of FreeSurfer and I haven?t been able to find &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; any threads for how to fix some of my problems. I have a very large &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; dataset and as I am editing on freeview I am noticing that ? or more &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; of my participants have a large area missing in the brainmask.mgz file &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; but the region is visible from the T1.file. In some participant scans &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; the areas missing arent too big however other scans (the photo I &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; attached) have a very large portion of the brain missing. I have tried &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; quite a few things to fix this including re running recon-all, adding &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; control points, and adjusting the wsthresh value, however, none have &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; worked. Wondering if there is a way to fix this kind of error and if &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; there is a way to prevent this from happening as I run recon-all on &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; future participants. In addition, I have been duplicating my files &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; before editing in order to always have the original files as a backup. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; With some participants when I duplicate the files their T1.mgz file &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ends up completely white (image attached). I have yet to see this in a &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; none duplicated file however with some participants I can duplicate &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; the files and have no issue. I have attached photos of both of my &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; problems. Any suggestions for fixes would be greatly appreciated. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Thanks, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Elana &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/59... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 11 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 11:31:47 -0400 &gt; &gt;&nbsp;&nbsp; &nbsp; From: "Douglas N. Greve"<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] Coregistration to MNI &gt; &gt;&nbsp;&nbsp; &nbsp; To: "Camargo, Aldo"<ACamargo@som.umaryland.edu&gt;&nbsp; <mailto:ACamargo@som.umaryland.edu&gt;, Freesurfer support &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<9af8c73e-46a8-e9b6-4b84-ce507589efed@mgh.harvard.edu&gt;&nbsp; <mailto:9af8c73e-46a8-e9b6-4b84-ce507589efed@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="windows-1252" &gt; &gt;&nbsp;&nbsp; &nbsp; It looks like cvs failed. Can you send the log? Also, please remember to post to the list and not us personally. &gt; &gt;&nbsp;&nbsp; &nbsp; On 7/30/2020 11:13 AM, Camargo, Aldo wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hi Douglas, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I was able to run the script to create the cvs folder and its files &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; but still I can not run the script that does the coregistration of the &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Pet image to the MNI space. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I am getting the following error: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; (base) &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; .0/S19445/subj1/mri$ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; mri_vol2vol --gcam &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; anPET.nii.gz &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; register.dof6.lta &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; $SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; $FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; pet.cvs.2mm.sm00.ni.gz Loading mov &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; anPET.nii.gz &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Loading source LTA register.dof6.lta &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ERROR: cannot find or read &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ---------------------------------------------------------------------- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; -- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *From:* Douglas N. Greve<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Sent:* Wednesday, July 29, 2020 10:39 AM &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *To:* Camargo, Aldo<ACamargo@som.umaryland.edu&gt;&nbsp; <mailto:ACamargo@som.umaryland.edu&gt;; Freesurfer support &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Subject:* Re: [Freesurfer] Coregistration to MNI Here is the command &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; mri_cvs_register --mov $subject --mni --openmp N &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; This command can take a very long time to run. The --openmp N &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; indicates the number of processors to use if you have a multiprocessor &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; system. Even with N=3, it can take 18 hours. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; On 7/29/2020 12:35 AM, Camargo, Aldo wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hi Douglas, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I don't have the folder cvs and I don't have the files bellow: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; How can I get these files, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Aldo &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; --------------------------------------------------------------------- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; --- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *From:* Camargo, Aldo<ACamargo@som.umaryland.edu&gt;&nbsp; <mailto:ACamargo@som.umaryland.edu&gt;&nbsp; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:ACamargo@som.umaryland.edu&gt;&nbsp; <mailto:ACamargo@som.umaryland.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Sent:* Monday, July 27, 2020 11:46 PM &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *To:* Douglas N. Greve<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&nbsp; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Subject:* Re: [Freesurfer] Coregistration to MNI Thanks a lot &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Douglas for your great input, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Aldo &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; --------------------------------------------------------------------- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; --- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *From:*freesurfer-bounces@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; on behalf of Douglas &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; N. Greve<dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt;&nbsp; <mailto:dgreve@mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Sent:* Monday, July 27, 2020 10:46 AM &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *To:*freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Subject:* Re: [Freesurfer] Coregistration to MNI This command will &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; allow you to have a registration file and sample into MNI152 2mm &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; space &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; mri_vol2vol --gcam pet.nii.gz register.dof6.lta &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; pet.cvs.2mm.sm00.nii.gz &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; you can get the registration file with mri_coreg --mov pet.nii.gz --s &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; $subject --reg register.dof6.lta &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hi Aldo, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; If you have a recon-ned structural MRI corresponding to your PET &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; scan then the answer is yes. &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Lilla &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; -------------------------------------------------------------------- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ---- &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *From:*freesurfer-bounces@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp; on behalf of &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Camargo, Aldo<ACamargo@som.umaryland.edu&gt;&nbsp; <mailto:ACamargo@som.umaryland.edu&gt;&nbsp; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:ACamargo@som.umaryland.edu&gt;&nbsp; <mailto:ACamargo@som.umaryland.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Sent:* Saturday, July 25, 2020 12:19 AM &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *To:* Freesurfer support list<freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; *Subject:* [Freesurfer] Coregistration to MNI &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ????????External Email - Use Caution &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Hi Freesurfer experts, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; I want to coregister a PET image to the MNI space, can I use &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; mri_cvs_register ? &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Thanks a lot, &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Aldo Camargo &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt;&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; The information in this e-mail is intended only for the person to whom &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; it is addressed. If you believe this e-mail was sent to you in error &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; and the e-mail contains patient information, please contact the &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; Partners Compliance HelpLine athttp://www.partners.org/complianceline%C2%A0; &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; . If the e-mail was sent to you in error but does not contain patient &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; information, please contact the sender and properly dispose of the &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; e-mail. &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/d9... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 12 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 17:39:06 +0200 &gt; &gt;&nbsp;&nbsp; &nbsp; From: Ellen Ji<ellen.ji@bli.uzh.ch&gt;&nbsp; <mailto:ellen.ji@bli.uzh.ch&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? labels? &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<24cc8874-81ee-1e68-85ad-b8fe662c4fc3@bli.uzh.ch&gt;&nbsp; <mailto:24cc8874-81ee-1e68-85ad-b8fe662c4fc3@bli.uzh.ch&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8"; format="flowed" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Dear experts, &gt; &gt;&nbsp;&nbsp; &nbsp; 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: &gt; &gt;&nbsp;&nbsp; &nbsp; mri_aparc2aseg \ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??????????????? --s subject1 \ &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; ??????????????? --annot 500_sym.aparc ? ??????????????? --wmparc-dmax 2 ? ??????????????? --labelwm ? ??????????????? --hypo-as-wm? ? ??????????????? --o subject1/mri/parcellation.nii.gz &gt; &gt;&nbsp;&nbsp; &nbsp; In fact, the output has 680 labels rather than 318 labels. A few questions. &gt; &gt;&nbsp;&nbsp; &nbsp; - 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 &gt; &gt;&nbsp;&nbsp; &nbsp; - 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) &gt; &gt;&nbsp;&nbsp; &nbsp; Thank you very much, &gt; &gt;&nbsp;&nbsp; &nbsp; Ellen &gt; &gt;&nbsp;&nbsp; &nbsp; ***** &gt; &gt;&nbsp;&nbsp; &nbsp; Ellen Ji, PhD &gt; &gt;&nbsp;&nbsp; &nbsp; Postdoctoral Research Fellow &gt; &gt;&nbsp;&nbsp; &nbsp; Psychiatric University Hospital &gt; &gt;&nbsp;&nbsp; &nbsp; University of Z?rich &gt; &gt;&nbsp;&nbsp; &nbsp; ellen.ji@bli.uzh.ch&nbsp; <mailto:ellen.ji@bli.uzh.ch&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; homanlab.github.io/ellen/ &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; Message: 13 &gt; &gt;&nbsp;&nbsp; &nbsp; Date: Thu, 30 Jul 2020 17:48:25 +0200 &gt; &gt;&nbsp;&nbsp; &nbsp; From: fsbuild<fsbuild@contbay.com&gt;&nbsp; <mailto:fsbuild@contbay.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Subject: Re: [Freesurfer] bad interpreter: No such file or directory &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? error &gt; &gt;&nbsp;&nbsp; &nbsp; To:freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Cc:marzbani91@gmail.com&nbsp; <mailto:marzbani91@gmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Message-ID:<1596124105.5f22ebc98f04a@trashmail.com&gt;&nbsp; <mailto:1596124105.5f22ebc98f04a@trashmail.com&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; Content-Type: text/plain; charset="utf-8" &gt; &gt;&nbsp;&nbsp;&nbsp; &nbsp; ??????? External Email - Use Caution &gt; &gt;&nbsp;&nbsp; &nbsp; Hello Hengameh, &gt; &gt;&nbsp;&nbsp; &nbsp; You probably need to install tcsh (and or csh). &gt; &gt;&nbsp;&nbsp; &nbsp; I would try, &gt; &gt;&nbsp;&nbsp; &nbsp; $&amp;nbsp;sudo&amp;nbsp;apt-get install csh tcsh &gt; &gt;&nbsp;&nbsp; &nbsp; - R.. &gt; &gt;&nbsp;&nbsp; &nbsp; On Jul 30, 2020, at 09:19, Hengameh Marzbani &amp;lt;marzbani91@gmail.com&amp;gt; wrote:&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;External Email - Use Caution&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;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&amp;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%C2%A0; <mailto:listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E; &gt; &gt;&nbsp;&nbsp; &nbsp; -------------- next part -------------- &gt; &gt;&nbsp;&nbsp; &nbsp; An HTML attachment was scrubbed... &gt; &gt;&nbsp;&nbsp; &nbsp; URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200730/87... &gt; &gt;&nbsp;&nbsp; &nbsp; ------------------------------ &gt; &gt;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt;&nbsp;&nbsp; &nbsp; End of Freesurfer Digest, Vol 197, Issue 59 &gt; &gt;&nbsp;&nbsp; &nbsp; ******************************************* &gt; &gt; &gt; &gt;&nbsp;&nbsp; &nbsp; _______________________________________________ &gt; &gt;&nbsp;&nbsp; &nbsp; Freesurfer mailing list &gt; &gt;&nbsp;&nbsp; &nbsp; Freesurfer@nmr.mgh.harvard.edu&nbsp; <mailto:Freesurfer@nmr.mgh.harvard.edu&gt; &gt; &gt;&nbsp;&nbsp; &nbsp; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer &gt; &gt; &gt; _______________________________________________ &gt; Freesurfer mailing list &gt; Freesurfer@nmr.mgh.harvard.edu &gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 4 Date: Fri, 7 Aug 2020 10:18:40 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edu&gt; Subject: Re: [Freesurfer] mri_vol2vol and diffusion issue To: <freesurfer@nmr.mgh.harvard.edu&gt; Message-ID: <a16871a9-4604-3a8c-cfcd-b83e9a1ff30b@mgh.harvard.edu&gt; 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: &gt; &gt; ????????External Email - Use Caution &gt; &gt; Hello! freesurfer experts, &gt; I am running dt_recon and mri_vol2vol to obtain FA values of five &gt; corpus callosum (CC) sub-regions. &gt; &gt; command1, dt_recon --b bvals.dat bvecs.dat --i &gt; $TUTORIAL_DIR/$subj/DTI/00001.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon &gt; &gt; ?command 2, mri_vol2vol --mov lowb.nii.gz \ &gt; &gt; --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ &gt; &gt; --inv --interp nearest --o $SUB?JECTS_DIR/$subj/mri/wmparc2diff.mgz \ &gt; &gt; --reg register.dat --no-save-reg &gt; &gt; ? Everything is OK after running the dt_recon command and the &gt; registration of all diffusion images with the anatomical data is good. &gt; However, some of my subjects show an issue with mri_vol2vol &gt; registration. When checking the wmparc2diff.mgz I created, it is &gt; apparent tha?t surfaces of lh.white and rh.white are not accurately &gt; mismatched with the wmparc2diff.mgz, as showed in the following &gt; figure. Is there an error with my command about mri_vol2vol or a &gt; problem in other aspects? ? ?Any advice with troubleshooting would be &gt; greatly appreciated.? Best Wishes ? Bo Tao M.D Student, Department of &gt; Radiology / Huaxi MR Research Center (HMRRC?West China Hospital of &gt; Sichuan University Chengdu? City, 610041? P.R. China? &gt; ?? ?? &gt; &gt; &gt; _______________________________________________ &gt; Freesurfer mailing list &gt; Freesurfer@nmr.mgh.harvard.edu &gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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End of Freesurfer Digest, Vol 198, Issue 11 *******************************************

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