Re: [Freesurfer] FreeSurfer coordinates

d.edu/fswiki/mri_label2label From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yang Yifan Sent: Friday, February 14, 2025 5:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer coordinates External Email - Use Caution Hi Yujing, Many thanks for your repl

Re: [Freesurfer] FreeSurfer coordinates

External Email - Use Caution Hi Yujing, Many thanks for your reply! The email didn’t come through to my inbox and I just found it in the online archive. Regarding the coordinate conversion, I had a look at the link but didn’t find MNI 305 related information. It would be very h

Re: [Freesurfer] FreeSurfer coordinates

The coordinates reported in .label are in Freesurfer tkregister RAS space. You can use mri_label2label to map them to MNI 305 space https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yang Yifan Sent: Wednesday, February 5

Re: [Freesurfer] FreeSurfer 8.0.0 beta error, while calculating the local gyrification index

This is a known issue when recon-all v8-beta is run a 2nd time. It will be fixed in the final v8 release. In the mean time, you can get around it with cd $SUBJECTS_DIR/subject/surf mris_compute_lgi --i lh.pial mris_compute_lgi --i rh.pial On 1/27/2025 5:59 AM, Katharina Wittfeld wrote:

Re: [Freesurfer] [freesurfer] recon-all error

it says finished without error On 1/15/2025 5:13 PM, 박경일 wrote:     External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the first time I’ve experienced an issue with this routine process. Please refer to the

Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data

*From:* Michael Eyre *Sent:* 11 January 2025 21:21 *To:* dgr...@mgh.harvard.edu *Subject:* Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data Hi, thanks for your response, apologies for late reply. nu.mgz

Re: [Freesurfer] Freesurfer crashing (gui) or exting with error (command line)

External Email - Use Caution  You don’t have permission to write to the default location of SUBJECTS_DIR as set in the freesurfer shell environment, i.e., /Applications/freesurfer/7.4.1/subjects.  The example subject data there is on purpose meant to be read only along with the

Re: [Freesurfer] Freesurfer remotely processing

External Email - Use Caution  The freesurfer mri* commands can be run from a terminal window remotely via ssh’ing into a machine that has access to a local installation of freesurfer.  Hopefully your network connection is robust enough to keep up with your typing in the terminal

Re: [Freesurfer] Freesurfer remotely processing

Hi Gonzalo Can you clarify what you mean? People use ssh all the time to log into remote machines and run recon-all (and freeview) Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Gonzalo Rojas Costa Sent: Monday, January 20, 2025 7:12 AM To: freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] Freesurfer Digest, Vol 251, Issue 6

External Email - Use Caution Thanks，please don't send emails！ > -原始邮件- > 发件人: freesurfer-requ...@nmr.mgh.harvard.edu > 发送时间:2025-01-06 22:12:15 (星期一) > 收件人: freesurfer@nmr.mgh.harvard.edu > 主题: Freesurfer Digest, Vol 251, Issue 6 > > Send Freesurfer mailing list submissio

Re: [Freesurfer] Freesurfer Digest, Vol 250, Issue 15

External Email - Use Caution no such email ，thanks 2025-01-01 05:31:40 freesurfer-requ...@nmr.mgh.harvard.edu 写道： > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://

Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data

For sub-04, can you look at the nu.mgz volume to see if that looks ok? Can you also see if the talairach registration looks ok? You should be able to run something like tkregisterfv --s subject --fstal It does not have to be perfect, but it is a problem if it is wildly off. On 12/29/2024 10:

Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data

-inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1 -threads 1 sub-31 rh best wishes Mike From: fsbuild Sent: 29 December 2024 23:22 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack sm

Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data

External Email - Use Caution  Signal 6 run time error indicates some kind of buffer overflow is expected to happen like the stack is going to be corrupted, and so the process is killed.  Please let us know the OS name and version you are running 8.0.0-beta on that produced the e

Re: [Freesurfer] freesurfer installation issues on debian

External Email - Use Caution I’m assuming you tried to install the freesurfer 7.4.1 release deb package for Ubuntu 22 which is available via the link,https://secure-web.cisco.com/1-8cAL3HeYSqkGt1gxwntnID8i3xh2XIP7o3oNj46aWRvzM1OdWL_6YCW3aou3M2mzul5sWVkT0j-Azlb9yR_oZD_Kfgg2a5lKMRz

Re: [Freesurfer] FreeSurfer Labels Question

Hi John It is mostly for background and other stuff outside of the brain Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Barsotti, Ercole Sent: Friday, December 13, 2024 5:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FreeSurfer Labels Question

Re: [Freesurfer] Freesurfer v8.0.0 error

I think this is the bug where you need to set the environment variable  FS_ALLOW_DEEP to 1, eg,  export  FS_ALLOW_DEEP=1 or  setenv FS_ALLOW_DEEP 1 Try that and then rerun On 12/11/2024 12:14 PM, Huang, Yujing wrote: Can you add those options as shown in the output ‘-fix-ento-wm -transfer-bas

Re: [Freesurfer] Freesurfer v8.0.0 error

Can you add those options as shown in the output '-fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph'? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ??? Sent: Wednesday, December 11, 2024 11:53 AM To: freesurfer@nmr.mgh.harv

Re: [Freesurfer] Freesurfer tutorial troubles

External Email - Use Caution The tutorial data exercises are not entirely up to date with the just announced beta release.   For now you could try running a pre 8.X stable dev build fromhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/stable/- or for your M2 Mac, you w

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

m the Docker Hub. From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of noga.ker...@campus.technion.ac.il <noga.ker...@campus.technion.ac.il> Sent: Wednesday, October 9, 2024 11:57 To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

noga.ker...@campus.technion.ac.il Sent: Wednesday, October 9, 2024 11:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .ltafile External Email - Use Caution Sorry, I forgot to attached it. Target, moving, moving_mask and the .lt

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

_ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of noga.ker...@campus.technion.ac.il Sent: Wednesday, October 9, 2024 03:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigidparameters from .ltafile External Email - Use Cauti

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

): could not allocate xforms And the temp_moved_mask.nii.gz is not generated Thanks, Noga From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Hoffmann, Malte,PhD Sent: Wednesday, October 9, 2024 03:22 To: Freesurfer support list Subject: Re: [Freesurfer

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

06 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from.lta file External Email - Use Caution Thanks You for the response! Another issue I encountered was with the .lta file that is being generated using mri_synthmorph. I want to use the .lta

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, October 1, 2024 17:12 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file You don't often get email fro

Re: [Freesurfer] Freesurfer stopped working after updating to Ubunto 24.04.1 LTS

External Email - Use Caution Hello Raj, Sometimes when OS’s update to a new major revision, the system libraries change such that software installed under the old OS version is not backwards compatible with the new OS version.  I think we may have already mentioned on the list t

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

? Thanks again, Noga From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, September 30, 2024 17:02 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file You don't

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, September 30, 2024 17:02 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

Use mri_coreg --mat2par file.lta On 9/29/2024 5:48 AM, noga.ker...@campus.technion.ac.il wrote: External Email - Use Caution Hello FreeSurfer Developers, I am using |mri_robust_register| to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a

Re: [Freesurfer] Freesurfer - skull stripping error

kef> Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Joshua K Lee Inviato: Sunday, September 29, 2024 5:53:01 PM A: Freesurfer support list Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error External Email - Use Caution I just want

Re: [Freesurfer] Freesurfer - skull stripping error

...@ucdavis.edu From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD Sent: Sunday, September 29, 2024 1:20 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer - skull stripping error You could try synthstrip, it might work

Re: [Freesurfer] Freesurfer - skull stripping error

Outlook per iOS<https://aka.ms/o0ukef> Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Fischl, Bruce R.,PHD Inviato: Sunday, September 29, 2024 4:20:00 AM A: Freesurfer support list Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error You

Re: [Freesurfer] Freesurfer - skull stripping error

rd.edu per conto di Fischl, Bruce R.,PHD Inviato: Sunday, September 29, 2024 4:20:00 AM A: Freesurfer support list Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error You could try synthstrip, it might work Cheers Bruce On Sep 29, 2024, at 7:38 AM, William Baare wrote:  Ex

Re: [Freesurfer] Freesurfer - skull stripping error

You could try synthstrip, it might work Cheers Bruce On Sep 29, 2024, at 7:38 AM, William Baare wrote:  External Email - Use Caution Hi Sara, You need to denoise the background. Here are some links that might be of help. Always check the quality of the output :-) https://github.com

Re: [Freesurfer] Freesurfer - skull stripping error

External Email - Use Caution Hi Sara, You need to denoise the background. Here are some links that might be of help. Always check the quality of the output :-) https://secure-web.cisco.com/11TUQn3ZMjB9gy2mI09erMcLASzJWGpSLFMUxf9tT-XFEDmLfZKdF-O_LIYc_Nlr6rt_zg2mZoh6G-ql4JyDGF9_GK

Re: [Freesurfer] FreeSurfer License Error

External Email - Use Caution  Since the last release of freesurfer 5.X in 2014, the encryption libraries on linux systems have changed such that the licenses downloaded for the current 7.X releases,https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads- cannot work with 5.X. I

Re: [Freesurfer] Freesurfer 7.4.0 and CUDA versions (was Re: (no subject))

External Email - Use Caution Thank you for the suggestions. It appears now to be seeing the DNN libraries. However, now I get: OOM when allocating tensor with shape[1,256,256,160,24] and type float on /job:localhost/replica:0/task:0/device:GPU:0 by allocator GPU_0_bfc My GPU has

Re: [Freesurfer] freesurfer version 6 on Debian

External Email - Use Caution  Debian 9 looks like it was the current version when Freesurfer 6 was released in 2017 for CentOS6 and MacOS.    But even if Freesurfer 6 runs on Debian 9, it’s not expected to run on current versions of Debian or CentOS because of system library cha

Re: [Freesurfer] FreeSurfer in fmriprep

: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer in fmriprep The log file says that recon-all finished without error. The command (robust register) was not called during recon-all. It must be called by fmriprep at some point. I don't understand what they are trying to d

Re: [Freesurfer] FreeSurfer in fmriprep

ow if more information is needed!  Thanks so much! Best, Tengwen *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, July 29, 2024 12:26 PM *To:* freesurfer@nmr.mgh.harvard.edu *Su

Re: [Freesurfer] FreeSurfer in fmriprep

Douglas N. Greve Sent: Monday, July 29, 2024 12:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer in fmriprep You don't often get email from dgr...@mgh.harvard.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> please sen

Re: [Freesurfer] FreeSurfer Question

please send your command line, terminal output, and stats file On 7/23/2024 3:07 PM, Selena Gangaram wrote: External Email - Use Caution Hi, I hope you are doing well, I subscribed to your mailing list to ask my question! I was wondering if you knew the reason as to why my extracti

Re: [Freesurfer] FreeSurfer in fmriprep

please send the recon-all.log file in the scripts folder On 7/23/2024 2:14 PM, Tengwen Fan wrote: External Email - Use Caution Dear FreeSurfer Developers, I hope this email finds you well! I am using fMRIprep to do pre-processing. The fMRIprep combines methodology from AFNI, ANTs, F

Re: [Freesurfer] freesurfer as module

External Email - Use Caution Thank you very much! From: fsbuild Sent: Tuesday, July 2, 2024 11:23 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freesurfer as module My understanding is that it is up to the sysadmins who run

Re: [Freesurfer] freesurfer as module

External Email - Use Caution  My understanding is that it is up to the sysadmins who run a cluster to choose how to present and configure the apps they host whether it be thru modules, spack, or other tools.  We don't track how cluster admins do that, but you could ask the helpd

Re: [Freesurfer] FreeSurfer atlases

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer atlases Try looking at it in freeview first. Some of the regions may be small, so you may have to hunt to get them. FYI you can specify nii as the output of mri_binarize On 6/28/2024 5:30 AM, Savoia, Alice (Stud. FPN) wrote: External Email - Use

Re: [Freesurfer] FreeSurfer atlases

have suggestions? Thanks, Alice *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, June 27, 2024 12:36 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FreeSurfer atlases I'm not sure wha

Re: [Freesurfer] FreeSurfer atlases

to open the mask in FSL I cannot visualize them. Does anyone have suggestions? Thanks, Alice From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, June 27, 2024 12:36 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesur

Re: [Freesurfer] FreeSurfer atlases

I'm not sure what you mean. We don't have an image of the subfields in, eg, mni space. Usually, you just run the subfield seg on the data that you want subfields for On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote: External Email - Use Caution Hello, I am looking for a freesufe

Re: [Freesurfer] freesurfer launching error

External Email - Use Caution  The info at the end of this posting about updating sshd_config in your Linux image might be helpful if you have not already tried it (enable X-forwarding, use local X11  host)https://stackoverflow.com/questions/62363023/x11-forwarding-from-wsl2-fail

Re: [Freesurfer] Freesurfer license

Hi Liz, Can you try adding a `-B ` to the `singularity run` command? -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ayoub, Lizbeth Sent: Monday, June 3, 2024 2:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer

Re: [Freesurfer] Freesurfer license

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Wighton, Paul Sent: Monday, June 3, 2024 12:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer license Hi Liz, What fmriprep container are you using and what are the full commands that are

Re: [Freesurfer] Freesurfer license

Hi Liz, What fmriprep container are you using and what are the full commands that are not working? Are you bind-mounting the freesurfer license file into the container via `singularity exec --bind`? -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

External Email - Use Caution Dear FS experts, I would like to follow up with the matter here - the T1.mgz isn't generated so I cannot inspect the image as instructed by the wiki page. I have checked the orientation on FreeView but it's correct. Would you please kindly advise?

Re: [Freesurfer] FreeSurfer Download and Install Error: Segmentation Fault

External Email - Use Caution  If you setup the Freesurfer environment ... here using bash and not zsh ... hostname ~ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.ci

Re: [Freesurfer] freesurfer doesn't work

External Email - Use Caution I've tried it. But, still freeview doesn't work -Original Message- From: "이준하" To: "Freesurfer support list"; Cc: Sent: 2024-04-14 (일) 20:22:40 (GMT+09:00) Subject: Re: [Freesurfer] freesurfer doesn't work

Re: [Freesurfer] freesurfer doesn't work

External Email - Use Caution I've tried it. But, still freeview doesn't work -Original Message- From: "fsbuild" To: ; Cc: Sent: 2024-04-14 (일) 06:04:32 (GMT+09:00) Subject: Re: [Freesurfer] freesurfer doesn't work External Email - Use Caut

Re: [Freesurfer] freesurfer doesn't work

External Email - Use Caution  If you have not already done so, please make sure your license.txt file has been setup in the shell for the freesurfer commands to read. Go to the URL below, fill out the form, and wait for license.txt to be emailed to the address you provided. https

Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution  You can try using the Silicon Mac development build on the M2 machine..  The download links is, https://secure-web.cisco.com/1sX8Y1I4GPyZJYzijtfGnav0Xe1MBg-Yv4HzZ07-_su8lv08rzyK4H8-8kXDApCOFJi1XX2mYF4_iH04jySngiX_PsKXZ8K48PCmsO5rOdoTp9xOkS_lWIvP4_shoz

Re: [Freesurfer] Freesurfer Waitlist

Title: WPForms External Email - Use CautionDear Sir/madam, Hope this email finds you well. I signed up in the waitlist earlier. May I know if there is still space for accommodating the waitlist participants? Thanks much. Cheers,Bess Sent from my iPhoneOn 21 Mar 2024, at 12:35 AM, La

Re: [Freesurfer] Freesurfer white matter overestimated

*Von:* Luisa Klahn *Gesendet:* Montag, 26. Februar 2024 08:53 *An:* dgr...@mgh.harvard.edu *Betreff:* Re: [Freesurfer] Freesurfer white matter overestimated Dear Douglas, Please find attached the pictures for the following issue: I

Re: [Freesurfer] Freesurfer white matter overestimated

It looks like the volume has very poor contrast. What volume are you displaying it on? Can you take a pic on the nu.mgz? On 2/26/2024 2:53 AM, Luisa Klahn wrote: External Email - Use Caution Dear Douglas, Please find attached the pictures for the following issue: I am processing struc

Re: [Freesurfer] Freesurfer white matter overestimated

Hi, no snapshots were attached. On 2/1/2024 6:02 AM, Luisa Klahn wrote: External Email - Use Caution Hello! I am processing structural data from a 3T scanner using Freesurfer version 7.3.2. For some subjects, the grey matter looks very thin, and the white matter looks overestimated.

Re: [Freesurfer] Freesurfer Intensity representation

See this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0 on multimodal integration. Basically, you will need to run mri_vol2vol to map your MPF volume to the anatomical/conformed space, then run mri_segstats passing it the segmentation you want to use and the converte

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: 16 January 2024 13:41 To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure The command should look like this ‘recon-all -s subjid -qcache -all -i input-file

Re: [Freesurfer] Freesurfer Intensity representation

External Email - Use Caution When MPF images are registered on T1 images, I think the intensity represents the MPF values, not the T1 values. This is because the registration process only transforms the spatial coordinates of the MPF images to match the T1 images, but does not alt

Re: [Freesurfer] Freesurfer Intensity representation

External Email - Use Caution I want to use the intensity of the macromolecular proton fraction (MPF). I want to compare the intensity of the MPF of the various brain regions or structures between two groups. I am not using the volumes. The MPF was registered on the T1 so does it m

Re: [Freesurfer] Freesurfer Intensity representation

External Email - Use Caution I want to use the intensity of the macromolecular proton fraction (MPF). I want to compare the intensity of the MPF between two groups. On Wed, Jan 24, 2024 at 6:11 PM Fischl, Bruce R.,PHD < bfis...@mgh.harvard.edu> wrote: > It is whatever volume you

Re: [Freesurfer] Freesurfer Intensity representation

It is whatever volume you gave as input to recon-all. If you tell us which statistics you want to regenerate for another volume we can tell you know what commands to run. cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Wednesday, January 24, 2024 9:05

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

The command should look like this 'recon-all -s subjid -qcache -all -i input-file' From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Monday, January 15, 2024 9:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache parti

Re: [Freesurfer] Freesurfer Digest, Vol 239, Issue 1

It looks like you are using MRS_200_UNI_MPRAGEised_stripped.nii for both the mov and the int. The int must be a full brain scan in registration with the slab. Also, it is better not to use --init-fsl (or any of the other --init-XXX flags) On 1/4/2024 9:21 AM, Spapens, Jeltje (NP) wrote:

Re: [Freesurfer] Freesurfer recon-all qcache partial failure

Your recon-all command doesn't have the directive to tell it what to run. You also need to specify input files for your initial run. See this wiki page for detail https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all The recon-all.log attached contains runs between 2009 and 2010 on subject 'fsav

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

Yes, that is correct On 12/20/2023 2:07 PM, Edwards, Vincent wrote: External Email - Use Caution Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer vers

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

Yes, that is correct. On 12/13/2023 3:01 AM, Edwards, Vincent wrote: External Email - Use Caution Hello, I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able

Re: [Freesurfer] freesurfer output stats

Hi Yunus The ones with “pial” in them are from the pial surface for things like curvature and surface area, the ones without are from the white surface. The rest of the name indicates which cortical parcellation the statistics are summarized in (e.g. the lh.aparc.pial.stats contains statistics

Re: [Freesurfer] Freesurfer Digest, Vol 238, Issue 7

External Email - Use Caution Hi I have not received a response to my question yet I think __ On 13/12/2023, 08.53, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of freesurfer-requ...@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer/Freeview Version Compatibility

External Email - Use Caution The freesurfer 6.X and 7.x release release notes summarize some changes for Freeview (listed below) since version 5 was released in 2013.   If none of the improvements in features/stability are relevant to what you are doing, then I don’t see why you

Re: [Freesurfer] FreeSurfer release for Redhat Linux 9.x and its clones

External Email - Use Caution We hope to have a binary rpm installer for CentOS9. I have not tried it, but the existing FS 7.4.1 CentOS8 binary rpm installer (https://secure-web.cisco.com/1mIKM9a0zhqsi_mcRwphvOt3o7Sjq5psvoHs9PCYVk-9pm31XnoNmc3uba-p0gcATG3DclmaBNOQlLGbQfbntyqmIFwtlf

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

list Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b External Email - Use Caution Hi Paul, Thank you so much for your confirmation! This is exactly what I’m having trouble with. In this case, maybe I can’t go with 7.3.1 and upper, I can go back to work with 7.1.1. Have you tried with

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

https://github.com/freesurfer/freesurfer/blob/dev/fsfast/bin/getmatlab -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Na, Xiaoxu Sent: Thursday, December 7, 2023 12:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Na, Xiaoxu mailto:x...@uams.edu>> Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b I believe the assumption is the freesurfer 7. 3. 1 distribution has already been installed (under /usr/local/freesurfer/7. 3

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

From: fsbuild mailto:fsbu...@contbay.com>> Sent: Wednesday, December 6, 2023 9:14 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Na, Xiaoxu mailto:x...@uams.edu>> Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b I believe the assumption is t

Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution   I believe the assumption is the freesurfer 7.3.1 distribution has already been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm linux installer file) and that FREESURFER_HOME is set in the environment  (/usr/local/freesurfer/7.3.

Re: [Freesurfer] FreeSurfer Parcellation Using Glasser's Atlas (HCP-MMP1)

Thank you! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Van

Re: [Freesurfer] FreeSurfer Parcellation Using Glasser's Atlas (HCP-MMP1)

External Email - Use Caution Sorry, missed this one before I got the personal invitation to respond. I believe this would use a FreeSurfer registration of the group parcellation to the individual. That is a folding-based registration and one can do slightly better than that wit

Re: [Freesurfer] freesurfer results QC

External Email - Use Caution Thanks a lot Kersten On Wednesday, November 22, 2023 at 02:04:33 PM GMT+3:30, Diers, Kersten /DZNE wrote: External Email - Use Caution Hi Yununs, thanks for your mail: There are no fixed and hard thresholds for these m

Re: [Freesurfer] freesurfer results QC

External Email - Use Caution Hi Yununs, thanks for your mail: There are no fixed and hard thresholds for these metrics (e.g., SNR). It really depends on the sample and image characteristics. More important than the absolute values is the distribution of these values across case

Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* 24 September 2023 05:22:56 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz External Email - Use Caution Ideally

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

External Email - Use Caution Hi there, yes, I can open an MRI volume just fine, using the code $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz But when it comes to surface files, it opens some of the surface files while crashing with other ones. Do you happen to know anything about

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

Can you load a MRI volume? From the crash report, it seems to be a system related issue that triggered the crash. Ruopeng On Oct 26, 2023, at 8:42 PM, Mirsol Choi mailto:mir...@ualberta.ca>> wrote: External Email - Use Caution Hi there, I have processed a t1 image using recon-all fu

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

External Email - Use Caution If you have been launching Freeview using the Finder by double clicking on the icon, then try running it from the command line in a terminal to open a file, e.g. in bash or zsh ... $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREE

Re: [Freesurfer] FreeSurfer License

External Email - Use Caution Hi Camille, https://secure-web.cisco.com/1Z0mtk-GdaneIrZnocCICBN5oOIERpgBztEHp89f1GbNPxyx9pDF2yKjprOTG9yU84m_9LhTGAI1I-cUYVbkQ16RRRJWIGiefjRgahDaYRPj7Zp_aYyD1X0FSo8PELG74pf8sPmJdMpwYYm3tSXGpJOKIQIYqASPUWsd6KlvqUtYuMS8Q-CBLmqvXh2_yglCkKUFf-7P-7yDqaccmf4

Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

External Email - Use Caution Ideally, you should have edited the aseg.presurf.mgz, then rerun recon-all starting just after the aseg. That said, if you edited the aseg.mgz and then re-ran that mri_segstats command, the stats should have changed. On 9/15/2023 4:05 AM, Krystal Xi

Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

External Email - Use Caution Dear FreeSurfer experts, I would like to further follow up with this issue - I tried to run the following command as instructed on https://secure-web.cisco.com/1DoD2qpUJoxGcDNOZSB1YhPJsD5GKpgHYq9R-yPlq1zTC_qaqWxFji3HTjaKE6hz8E9Az-p_XziNeB7-nmb2je3J9g

Re: [Freesurfer] freesurfer data analysis and visualization

External Email - Use Caution I'm not sure what you are asking for. The freeview command allows you to view volumes in 3D On 9/6/2023 12:50 PM, Pukovisa Prawiroharjo wrote: External Email - Use Caution anyone have suggestion data visualization from freesurfer volumetric

Re: [Freesurfer] FreeSurfer hippo-amygala module

External Email - Use Caution Thanks for the interest in our work, Anton! We don’t have a template in MNI space, sorry (it’s on the to-do list, but buried among many other items). But you can always segment the template with the atlas 😃 Cheers, /Eugenio -- Juan Eugenio Iglesias h

Re: [Freesurfer] Freesurfer issue

External Email - Use Caution  Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For

Re: [Freesurfer] Freesurfer Virtual Machine Password Request

External Email - Use Caution Hello, Thanks for offering to help out. I need help in these two areas. 1. Password to open the downloaded zip file that contains the Ubuntu+ free surfer image. 2. Password to open the image in virtual box. As per the doc I am referring, our username

Re: [Freesurfer] Freesurfer version and Installation

External Email - Use Caution  The mri_synthsr script in the 7.4.1 release from June 2023 offers 3 models - one version 1.0 model and two version 2.0 models (depending upon the arguments).  The default in the absence of any qualifying arguments is the general version 2 model. - R

Re: [Freesurfer] Freesurfer version and Installation

External Email - Use Caution Hello, Thank you for your response. I have an additional question: I am utilizing Synthsr version 2.0. Is this particular version included in The 7.4.1 version of freeusrfer? Regards Hengameh From: freesurfer-boun...

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