17 Aug
2020
17 Aug
'20
10:17 a.m.
I think too much time has passed, and the file was deleted. Can you re-upload?
On 8/14/2020 10:10 PM, Elana Sarabin wrote:
External Email - Use Caution
I believe the file was uploaded. The name is subj-32.tar.gz.
Thanks,
Elana
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, August 13, 2020 at 7:52 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Recon-all Soft Errors
[△EXTERNAL]
This is a tarball of all your dicoms. Please send us the contents of the output of recon-all (the subject's folder) following in the instructions below.
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 8/9/2020 11:25 AM, Elana Sarabin wrote:
* External Email - Use Caution * I have attached the file which corresponds to the image I sent earlier. Let me know if you need to see anything else. Thanks, Elana *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edu> <mailto:BFISCHL@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Saturday, August 8, 2020 at 10:24 AM *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Recon-all Soft Errors [△EXTERNAL] Hi Elana You say it happens on 50% of your participants. Can you pick one and upload the entire gzipped and tarred directory for that subject? Cheers Bruce *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Elana Sarabin *Sent:* Saturday, August 8, 2020 10:07 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Recon-all Soft Errors * External Email - Use Caution * Sorry I’m not sure I know what you mean when you say an example dataset. Regards, Elana Get Outlook for iOS <https://aka.ms/o0ukef> ------------------------------------------------------------------------ *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu <mailto:BFISCHL@mgh.harvard.edu>> *Sent:* Friday, August 7, 2020 9:17:24 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> *Subject:* Re: [Freesurfer] Recon-all Soft Errors [△EXTERNAL] Can you upload an example dataset? It looked like an intensity normalization failure that probably caused a topological defect Cheers Bruce *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *On Behalf Of *Elana Sarabin *Sent:* Friday, August 7, 2020 11:08 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> *Subject:* Re: [Freesurfer] Recon-all Soft Errors * External Email - Use Caution * More so that the brainmask.mgz is missing a lot of both grey and white matter. For some the area cut out in brainmask is much smaller and for others it is large just like the photo I sent. I am wondering if there is a way to fix this since 50% of my participants scans look like this. Thanks, Elana Get Outlook for iOS <https://aka.ms/o0ukef> ------------------------------------------------------------------------ *From:*freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> *Sent:* Friday, August 7, 2020 8:17:42 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> *Subject:* Re: [Freesurfer] Recon-all Soft Errors [△EXTERNAL] 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@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Tuesday, August 4, 2020 at 8:01 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@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@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Offreesurfer-request@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@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@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@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@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@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. 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