Re: [Freesurfer] Segmentation White matter bad

2024-02-26 Thread Douglas N. Greve
I can't tell from those pics what is happening. Does it look like an imaging artifact? You can try putting control points On 2/26/2024 12:58 PM, lejia2011411409 wrote: External Email - Use Caution Hi,   I used command:  recon-all  -s subject1 -i subject1.nii   -all -sd  /home/t1. I t

Re: [Freesurfer] Segmentation White matter bad

2024-02-26 Thread lejia2011411409
External Email - Use Caution Hi, I used command: recon-all -s subject1 -i subject1.nii -all -sd /home/t1. I think it is FrreSurfer default method to segementation. Lejia At 2024-02-27 01:24:00, "Douglas N. Greve" wrote: what did you use the do the segmentation?

Re: [Freesurfer] Segmentation White matter bad

2024-02-26 Thread Douglas N. Greve
what did you use the do the segmentation? Include command line and terminal output On 2/26/2024 10:46 AM, lejia2011411409 wrote: External Email - Use Caution Dear freesurfer experts, A large amount of subjects got segmentation white matter bad (some dark white matter cannot be recog

Re: [Freesurfer] Segmentation error with T2w

2023-12-06 Thread Huang, Yujing
Hi Jakob, I believe we fixed the bug in FS 7.4 release. Can you give it a try? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Litsch, Jakob Benjamin Sent: Wednesday, December 6, 2023 10:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segmentation error w

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2023-11-17 Thread Joshua Ezequiel Pasaye
n.edu<mailto:joshua.pas...@northwestern.edu> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Date: Friday, November 17, 2023 at 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the am

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2023-11-17 Thread Iglesias Gonzalez, Juan E.
Dear Joshua, This is a bit of an empirical question. I’d totally run both on a few subjects and compare the results. If you do so: I would selfishly/greatly appreciate it if you shared your impressions with me :-) Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesur

Re: [Freesurfer] Segmentation fault (core dumped)

2023-03-09 Thread fsbuild
External Email - Use Caution As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and binary backwards compatibility cannot be expected to work indefinitely going forwards to newer versions of the OS.  I ran a simple mri_surf2surf command from 5.1.0 on CentOS7

Re: [Freesurfer] Segmentation fault (core dumped)

2023-03-06 Thread Huang, Yujing
Hi Tracy, I’m wondering if you have any success with other subjects. Can you attach the failed recon-all.log? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Tracy Riggins Sent: Sunday, March 5, 2023 1:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segm

Re: [Freesurfer] Segmentation of hippocampus(left), grey and white matter regions.

2022-11-10 Thread Nolan, Jackson
Hello, If you have T1 images that have been processed with FreeSurfer, you can use the script 'segmentHA_T1.sh' to automatically segment hippocampal subfields. Best, Jackson From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of PRASAD D Sent: Monday, Octo

Re: [Freesurfer] Segmentation of hippocampus(left), grey and white matter regions.

2022-11-08 Thread Douglas N. Greve
Try running recon-all on the unskull stripped data. Alternatively, if  you just want hippo you can run mri_synthseg or samseg On 10/31/2022 5:32 AM, PRASAD D wrote: External Email - Use Caution Hello everyone. I’m new to FREESURFER I would like to segment the sMRI images. I have ext

Re: [Freesurfer] Segmentation Fault (Ventura)

2022-11-07 Thread fsbuild
External Email - Use Caution Hello Joann, If I read correctly, you are doing a remote mount of a shared network drive to your Mac to store/read/write the subject files but running the recon-all using your Mac processors. You might want to check the directory for the last subject

Re: [Freesurfer] Segmentation fault: 11

2022-10-05 Thread fsbuild
External Email - Use Caution Hello Priya, It could help to know,- the version of freesurfer you installed, e.g., the latest 7.3.2 release from https://secure-web.cisco.com/1zdcvVhqKzcbDdvruGd5f9eNe1UebLwxcHQNPPf-imCCfHdpe0i9n7VbHnkOmApVqwXLBFsNTr00VNAx6komIIAOhuIRk6xXYWHGaglPYJch

Re: [Freesurfer] Segmentation protocol used by Freesurfer

2022-08-30 Thread Fischl, Bruce
It really can be anything. Hard to say From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ruifeng Dong Sent: Tuesday, August 30, 2022 3:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer External Email - Use Caution Thanks. I

Re: [Freesurfer] Segmentation protocol used by Freesurfer

2022-08-30 Thread Ruifeng Dong
in a structure can change (e.g. > is the fimbria part of the hippocampal label?) > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ruifeng Dong > *Sent:* Tuesday, August 30, 2022 2:34 PM > *To:* Free

Re: [Freesurfer] Segmentation protocol used by Freesurfer

2022-08-30 Thread Fischl, Bruce
...@nmr.mgh.harvard.edu On Behalf Of Ruifeng Dong Sent: Tuesday, August 30, 2022 2:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer External Email - Use Caution Thanks, Bruce. Actually, I am comparing the volume computations between

Re: [Freesurfer] Segmentation protocol used by Freesurfer

2022-08-30 Thread Ruifeng Dong
External Email - Use Caution Thanks, Bruce. Actually, I am comparing the volume computations between different segmentation tools. In some software's paper, they mentioned there is a slight difference in protocol from Freesurfer and thus not easy to compare. I am wondering what th

Re: [Freesurfer] Segmentation protocol used by Freesurfer

2022-08-30 Thread Fischl, Bruce
Hi Ruifeng I think they are similar, but you would have to ask Neuromorphometrics about the differences. Our protocol was published in the Neuron 2002 paper and the papers it cites, which I think is also where the Neuromorphometrics’ protocol came from Cheers Bruce From: freesurfer-boun...@nm

Re: [Freesurfer] segmentation of thalamic nuclei: possibility of generating connectome

2022-08-08 Thread Yendiki, Anastasia
Hi Lauren - What you want is to replace the thalamus labels in aparc+aseg.mgz with the thalamic nuclei labels. This is a bit less straightforward than it may first seem because the outer boundaries of the thalamus in the two segmentations are not necessarily the same. However, we've implemented

Re: [Freesurfer] Segmentation Mistakes

2022-07-10 Thread Douglas N. Greve
what are you using as input? I can't tell from the image you sent, but it looks pretty blurry. What is the resolution? What kind of acquistion? On 6/28/2022 11:38 PM, Wang, Yu wrote: External Email - Use Caution Hello FreeSurfer Developers, I used the _recon-all -s c1NT816 -i smwrc1N

Re: [Freesurfer] segmentation corpus callosum

2022-07-03 Thread Fischl, Bruce
Sure, just run your subject through recon-all, then use mri_binarize or mri_extract_label to pull the cc labels out of the aseg. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Mostafa Fakhri Sent: Sunday, July 3, 2022 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject:

Re: [Freesurfer] segmentation fornix with mri_cc

2022-06-27 Thread Douglas N. Greve
I'm not sure that will work. You should use mri_sclimbic_seg https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic On 6/27/2022 3:31 AM, Mostafa Fakhri wrote: External Email - Use Caution Hello to all of you I ran recon-all: $ recon-all -sd /share/users/mfakhri/FS/subjects -subject 1021

Re: [Freesurfer] Segmentation of thalamic nuclei

2021-11-16 Thread Iglesias Gonzalez, Juan E.
Hi Katie, This is weird. Does /home/bdl/freesurfer/subjects/SD027/scripts/ exist? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 16 Nov 2021, at 17:19, Katherine Andrade mailto:kandrade8...@sdsu.edu>> wrote:

Re: [Freesurfer] Segmentation of thalamic nuclei - misplaced position

2021-10-14 Thread Iglesias Gonzalez, Juan E.
Dear Edyta, The smaller nuclei are definitely less accurate than the bigger ones in the atlas. Is it only the VM giving you trouble? Is it in every case, or only on this case? Cheers, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeigle

Re: [Freesurfer] Segmentation fault (core dumped) of freeview

2021-10-13 Thread fsbuild
External Email - Use Caution Hello Yuhui, Did you try something like the following (from https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek8hQagKNFY9pH9jg_UzrEMFBjBl1Lo36JvBnp02E7HopuMgcNTaG0pTRx-2PR61unk8dCsv-4Gp50vSlBbeEJzjsRZGWS1jqAp0pVmSzDy9Ob23Rg1PB3s

Re: [Freesurfer] Segmentation of thalamic nuclei: LGN volume

2021-09-19 Thread Iglesias Gonzalez, Juan E.
Thanks, Marco. The volume of the LGN in our atlas is ~215mm3. Volume discrepancies with other atlases or manual tracing are common, particularly for such small nuclei with faint contrast (and also due to discrepancies in criteria eg to determine the posterior / medial boundary with the rest of

Re: [Freesurfer] Segmentation of thalamic nuclei: LGN volume

2021-09-16 Thread Marco Aiello
External Email - Use Caution Dear Eugenio, Thank you. I've uploaded via FTP a zip file (g1120_5.zip) containing a recon-all folder of a subject, including thalamic nuclei segmentation. Best, Marco Il giorno lun 30 ago 2021 alle ore 10:17 Marco Aiello < marcoaiello1...@gmail.c

Re: [Freesurfer] Segmentation of thalamic nuclei: LGN volume

2021-08-30 Thread Iglesias Gonzalez, Juan E.
Hi Marco, Would you mind sharing a representative case with us, please? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Aug 30, 2021, at 04:17, Marco Aiello mailto:marcoaiello1...@gmail.com>> wrote: Ext

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Thanks!!! Kind regards, Rosie El mié., 7 jul. 2021 21:32, Paul Wighton escribió: > External Email - Use Caution > > Hi Rosie, > > In that case, you can try running the v6 version of hippocampal subfields, > e.g: > > recon-all -s sub-002_ses-

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Paul Wighton
External Email - Use Caution Hi Rosie, In that case, you can try running the v6 version of hippocampal subfields, e.g: recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1 -Paul On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo wrote: > External Email - Use Caut

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Hi Paul, Thank you. The think is that I already run recon-all in all the participants and I made some corrections (control points,...). I just want the hipocampal subfields...What should I do in this case scenario? El mié., 7 jul. 2021 21:03, Paul

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Paul Wighton
External Email - Use Caution Thanks Rosie, that explains it. You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is not in this version. There are two options. If you want to continue using v6.0.0, you can refer to the instructions here: https://secure-web.cis

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Here it is: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-st

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Paul Wighton
External Email - Use Caution Ok, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason. You should be able to confirm that by running: ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh Does it say something like? ls: cannot access '/usr/local/frees

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Hi Nayan, Do you mean this? rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $ On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani wrote: > External Email - Use Caution > > Dear Rosalia, > > Once y

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread nayan wadhwani
External Email - Use Caution Dear Rosalia, Once you export and source freesurfer with the following commands export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh type sh after sourcing and then try running it(without closing the terminal) hopef

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Hi Paul, I did it: # FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh And I even re-started the computer b

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Paul Wighton
External Email - Use Caution Sure Rosie, no worries. Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'): export PATH=${FREESURFER_HOME}/bin:${PATH} After saving, close all your terminal windows,

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Hi Paul, Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder. When I do what you ask me to do: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosali

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-07 Thread Paul Wighton
External Email - Use Caution Hi Rosie, The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory. If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_H

Re: [Freesurfer] Segmentation of hippocampal subfields

2021-07-06 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Following this more actualized link: https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoT

Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

2021-02-24 Thread Roman Fleysher
behalf of Roman Fleysher Sent: Tuesday, February 23, 2021 12:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do

Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

2021-02-23 Thread Roman Fleysher
do not know details. Thank you, Roman From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Roman Fleysher Sent: Tuesday, February 23, 2021 10:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentation is shifted with respect to

Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

2021-02-23 Thread Roman Fleysher
) have the same issue. Looking into these. Roman From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, February 23, 2021 10:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentation is shifted with respect

Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

2021-02-23 Thread Douglas N. Greve
Those commands look right On 2/23/2021 9:27 AM, Roman Fleysher wrote: External Email - Use Caution Dear FreeSurfers, I am working with version 6, starting point is T1W image in NIFTI format. I typically transform segmentations back to native space in NIFTI format to be able to use o

Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

2021-01-14 Thread Greve, Douglas N.,Ph.D.
, Kevin Date: Tue, 12 Jan 2021 15:45:37 + From: "Greve, Douglas N.,Ph.D." mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0 To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesu

Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

2021-01-12 Thread Dowling, Kevin Francis
+ From: "Greve, Douglas N.,Ph.D." mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0 To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurf

Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

2021-01-12 Thread Greve, Douglas N.,Ph.D.
For some reason, it is not capturing the terminal output in the log files. Can you just run mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz and send me the terminal output? On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote: Hello FreeSur

Re: [Freesurfer] segmentation fault

2021-01-03 Thread Greve, Douglas N.,Ph.D.
Please send the recon-all.log file On 12/25/2020 8:42 PM, Wei Koo wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon2 for a number of subjects, but one of my subjects I get the following error when I run the mri_tesellate command: Removing int

Re: [Freesurfer] Segmentation of hippocampus and amygdala: using an additional scan with low-pixel

2020-09-14 Thread ­최선아 / 학생 / 뇌인지과학과
External Email - Use Caution Thank you for your advice! Best regards, Sunah. 2020년 9월 14일 (월) 오후 9:50, Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu>님이 작성: > Dear Sunah, > > I would use the T1 alone. > > Cheers, > > /E > > > > > > Juan Eugenio Iglesias > > Senio

Re: [Freesurfer] Segmentation of hippocampus and amygdala: using an additional scan with low-pixel

2020-09-14 Thread Iglesias Gonzalez, Juan E.
Dear Sunah, I would use the T1 alone. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of ­최선아 / 학생 / 뇌인지과학과 Reply-To: Freesurfer support list Date: Monday, September 14, 2020 at 03:16 To: "freesurfer@nm

Re: [Freesurfer] Segmentation of CT Scans

2020-08-27 Thread Douglas N. Greve
You can try running samseg on it (in version 7.1.1), eg samseg --i ct.nii.gz --o samseg Then look at samseg/seg.mgz I have no Idea what will happen, but samseg is pretty robust, so it might work On 8/27/2020 4:53 AM, mudassar liaq wrote: External Email - Use Caution Hi,   As far as I

Re: [Freesurfer] Segmentation with FreeSurfer 7.1

2020-07-15 Thread Douglas N. Greve
I don't. My guess is that there is a tolpolgical default there that is not fixed correctly in 7.1. Sometimes these things are on the edge and slight changes will affect them. On 7/13/2020 4:22 AM, Sara PONTICORVO wrote: External Email - Use Caution Dear FreeSurfer experts, we are pe

Re: [Freesurfer] Segmentation Issues

2020-03-24 Thread Bruce Fischl
Hi Harriet it's tough to diagnose from just this, but that is pretty bad! Can you give us some details about the editing? Or tar/gzip the whole subject dir and upload it and we will take a look cheers Bruce On Tue, 24 Mar 2020, Harriet Cornwell wrote: External Email - Use Cautio

Re: [Freesurfer] Segmentation Fault during recon-all using FLAIR Image

2020-01-16 Thread Greve, Douglas N.,Ph.D.
It is seg faulting at the defect correction stage which is before the FLAIR would be used. At this point it should be identical to the T1-only analysis. Check your commands to make sure they are the same except for the FLAIR part On 1/16/2020 9:55 AM, Swanson,Clayton wrote: External Ema

Re: [Freesurfer] Segmentation fault mri_em_register

2019-12-13 Thread Bruce Fischl
Hi Ricardo hmmm, the fact that it says "MRImaskDifferentGeometry" suggests that your skull stripping didn't end up "conforming", which is probably the error. Try something like: cp brainmask.mgz brainmask.bet.mgz mri_convert -rl orig.mgz brainmask.bet.mgz brainmask.mgz then rerun and see if

Re: [Freesurfer] Segmentation faule recon-all

2019-10-04 Thread Greve, Douglas N.,Ph.D.
Did you check the talairach transform? See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview On 10/4/2019 1:37 PM, Backhausen, Lea wrote: External Email - Use Caution Dear FreeSurfer experts, when running the recon -all –all command (I included the -3T flag) with

Re: [Freesurfer] Segmentation fail

2019-08-28 Thread Greve, Douglas N.,Ph.D.
recon-all does not do so well with data at 0.5mm. I created a high-res patch for version 6.0 as part of my support fo r the HCP. You can get it here https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp this shold work much better. On 8/27/19 10:15 AM, Giovana dos Santos Cover w

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2019-06-05 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Yes! The changes will probably be tiny, though. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Boris Rauchmann Reply-To: Freesurfer support list

Re: [Freesurfer] Segmentation fault

2019-03-14 Thread Donatienne Van Weehaeghe
namens Greve, Douglas N.,Ph.D. Verzonden: donderdag 14 maart 2019 17:17:54 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Segmentation fault Can you send the command line with out variables and the full terminal output? On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote

Re: [Freesurfer] Segmentation fault

2019-03-14 Thread Greve, Douglas N.,Ph.D.
t; > --no-rescale --threads 8 > > Kind regards > > Donatienne > > > // > > > *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > namens Tim Schäfer > > *Verzonden:* woensdag 13 maart 2019 23:22:07 > *Aan:* Frees

Re: [Freesurfer] Segmentation fault

2019-03-14 Thread Donatienne Van Weehaeghe
/gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 Kind regards Donatienne Van: freesurfer-boun...@nmr.mgh.harvard.edu namens Tim Schäfer Verzonden: woensdag 13 maart 2019 23:22:07 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer

Re: [Freesurfer] Segmentation fault

2019-03-13 Thread Tim Schäfer
External Email - Use Caution > On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe > wrote: > The code I tried to run: > > #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg > /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o > gtmpvc.output.su

Re: [Freesurfer] segmentation error

2019-02-21 Thread mara alves
External Email - Use Caution Hi there, Just want to check if you get the recon-all files that I sent for an entire subject?! I am also wondering if the problem with the segmentation can be related to the small size of aged Portuguese brains considering the expected size based for

Re: [Freesurfer] segmentation problem

2019-01-10 Thread Bruce Fischl
Hi Manuela you can certainly do manual editing in freeview cheers Bruce On Thu, 10 Jan 2019, Manuela Costa wrote: External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation.  Unfortunately,

Re: [Freesurfer] Segmentation Query

2018-12-14 Thread Bruce Fischl
Hi Fariha The number of regions is based on the anatomy. You can combine them if you like. The volume to use is probably the aparc+aseg.mgz, which is easily convertible to .nii with mri_convert. Also, you should use freeview not tkmedit (tkmedit has been deprecated for many years) cheers B

Re: [Freesurfer] Segmentation Query

2018-12-13 Thread Fariha Muazzam
External Email - Use Caution Hi Bruce I am working on segmentation of brain regions. I wanted to know: 1. If it is possible that I could get brain segmented into 8 regions or maybe 20, because when I segmented using recon-all command, I got segmentation of 45 regions ? 2. I was loo

Re: [Freesurfer] Segmentation Query

2018-12-13 Thread Bruce Fischl
Hi Fariha can give us more details? How would you like to customize them? I think the answer is probably no, but I'm not sure I understand what you are trying to do cheers Bruce On Wed, 12 Dec 2018, Fariha Muazzam wrote: External Email - Use Caution Hi I am working in

Re: [Freesurfer] Segmentation of hippocampal subfields on FS v6 stable data?

2018-11-30 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module on the 6.0-reconned data. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and

Re: [Freesurfer] Segmentation fault

2018-11-19 Thread Whitney, Jon
External Email - Use Caution Update - Segmentation fault I think I have finally found the issue. The bvec files I uploaded actually contained only zeroes for each bvec value, and that made it impossible for Tracula to function properly. This was a result of the original files w

Re: [Freesurfer] Segmentation fault

2018-10-31 Thread Whitney, Jon
External Email - Use Caution I probably deleted the log file prior to running the path step so I could focus on what was going on. I'll re-run it and give you the results when it finishes. Thanks! -- Notice: This e-mail message, together with any attachments, contains informat

Re: [Freesurfer] Segmentation fault

2018-10-31 Thread Yendiki, Anastasia
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, October 31, 2018 at 9:57 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Segmentation fault

Re: [Freesurfer] Segmentation of thalamic nuclei - no reticular nucleus

2018-10-30 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Hi HSK We use it in the model fitting but do not segment it due to the absolute lack of contrast with the white matter. Kind regards, Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedic

Re: [Freesurfer] Segmentation fault

2018-10-30 Thread fsbuild
External Email - Use Caution ​Hello Jon, Since trac-all is a tcsh script, you could try prefacing it with "tcsh -x" to get extra output about what it is doing, i.e., $ tcsh -x trac-all  rest of args... - and then look thru the trac-all output to see where it actually runs a bi

Re: [Freesurfer] Segmentation fault

2018-10-29 Thread fsbuild
External Email - Use Caution ​Hello Jon, Looks like you are already running with -debug and -allowcoredump option, and the shell limits do not look like they are too small to allow the coredump to be written.  I don't know offhand if that coredump option causes a file to be wri

Re: [Freesurfer] Segmentation fault

2018-10-28 Thread fsbuild
External Email - Use Caution Hello Jon, Can you get any stack or backtrace information after the segfault occurs ?, e.g., Mac OS has the option to display the crash report with a trace.  On Linux you could run thru gdb and get a back trace.   This would help us to see where the

Re: [Freesurfer] Segmentation issue with FS6

2018-04-24 Thread Bruce Fischl
Hi Cody yes, it could be due to poor contrast. The watershed isn't the issue though, it is mri_segment and mris_make_surfaces. You can try changing the wm/gm limits, or upload the subject and we will take a look cheers Bruce On Tue, 24 Apr 2018, Barlow, Cody wrote: External Email

Re: [Freesurfer] Segmentation of anterior and posterior commissures

2018-04-14 Thread Bruce Fischl
Hi Antonin unfortunately the atlas subjects were not collected with an IRB that allows us to distribute them. We are working to update the atlas with data we can distribute, but that is not a short-term solution. You second proposal would work I imagine cheers Bruce On Sat, 14 Apr 2018, Antoni

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2018-01-09 Thread Carme Uribe Codesal
Great! Thanks! 2018-01-08 16:44 GMT+01:00 Hoopes, Andrew : > Hi Carme, > > segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh. > harvard.edu/pub/dist/freesurfer/dev > > best, > Andrew > > > On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal > wrote: > > Dear FreeSurfer users,

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2018-01-08 Thread Hoopes, Andrew
Hi Carme, segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev best, Andrew On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal mailto:carme.ur...@gmail.com>> wrote: Dear FreeSurfer users, I wanted to run the new script that segments the h

Re: [Freesurfer] Segmentation fault (core dumped)

2017-12-21 Thread Douglas N Greve
N Greve > > *Sent:* Monday, December 18, 2017 5:09:25 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Segmentation fault (core dumped) > > We need more details. Try looking at this web site > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >

Re: [Freesurfer] Segmentation fault (core dumped)

2017-12-18 Thread Douglas N Greve
We need more details. Try looking at this web site surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 12/18/2017 04:08 PM, Uquillas, Federico D'Oleire wrote: > > Dear FreeSurfer experts, > > > I am unable to run the qcache procedure and was wondering if anybody > could help me find what is goi

Re: [Freesurfer] Segmentation fault (core dumped)

2017-12-18 Thread Uquillas, Federico D'Oleire
Dear FreeSurfer experts, I am unable to run the qcache procedure and was wondering if anybody could help me find what is going on. I've tried running qcache with several versions of the fsaverage (e.g., fsaverage5, fsaverage6, fsaverage), and have also tried running it in a variety of subjec

Re: [Freesurfer] Segmentation Volume to Cortical Labels

2017-11-25 Thread Douglas Greve
try mris_seg2annot Run it with --help to get examples On 11/13/17 3:06 PM, Hengda He wrote: Hi Freesurfer Developers, I have a manually edited segmentation of the brain cortical regions, and I want to map it to cortical parcellation labels on both white matter surface and pial surface. So I

Re: [Freesurfer] Segmentation Volume to Cortical Labels

2017-11-13 Thread Bruce Fischl
Hi Hengda yes, I think you can either use mri_vol2surf or mris_sample_parc to get your segmentation onto the surface cheers Bruce On Mon, 13 Nov 2017, Hengda He wrote: > Hi Freesurfer Developers, > > I have a manually edited segmentation of the brain cortical regions, and I > want to map it t

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Douglas N Greve
help, > Idil > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 25, 2017 11:00 PM > To: freesurfer@nmr.mgh.harvard.edu > Su

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Yagmur Ozdemir 19
] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files what is your command line? On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote: > When I do either of the conversions with mris_convert, the system gi

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Yagmur Ozdemir 19
...@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files what is your command line? On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote: > When I do either of the conversions with mris_convert, the sys

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Douglas N Greve
t; Best, > Idil > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 25, 2017 10:21 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Segmenta

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Yagmur Ozdemir 19
...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files you can convert the overlays directly to nifti, but they aren't surfaces - they are scalar f

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Bruce Fischl
r-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 25, 2017 7:47 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Segmentation Violation problem in surface files > > Hi Idil > > I'm not sure what you m

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Yagmur Ozdemir 19
Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files Hi Idil I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 20

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Bruce Fischl
rvard.edu] > Sent: Monday, July 24, 2017 10:36 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Segmentation Violation problem in surface files > > Hi Idil, > > we only store surface overlays in .mgz not surfaces themselves. Try loading > a surface (like lh.infl

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-25 Thread Yagmur Ozdemir 19
-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files Hi Idil, we only store surface overlays in .mgz not surfaces themselves. Try loading a su

Re: [Freesurfer] Segmentation Violation problem in surface files

2017-07-24 Thread Bruce Fischl
Hi Idil, we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote: > Hello freesurfer experts, > > I am trying to use

Re: [Freesurfer] Segmentation problem recon-all

2017-06-22 Thread Bruce Fischl
I see. Yes, that kind of thing is hard. YOu can try the gcuts skullstripping, which is more aggressive and can sometimes get rid of this kind of thing, but it also is more likely to strip brain. Or manually remove those voxels in the brainmask.mgz cheers Bruce On Thu, 22 Jun 2017, Lisa Delal

Re: [Freesurfer] Segmentation problem recon-all

2017-06-22 Thread Lisa Delalande
Hi Bruce, Thank you very much for your mail. I am going to specify my question. In fact, we saw a problem after the recon-all step. The dura was included in the lh.pial and rh.pial. Indeed, the red demarcation included the meninges. I send you an attachment Cheers Marine 2017-06-21 18:51

Re: [Freesurfer] Segmentation problem recon-all

2017-06-21 Thread Bruce Fischl
Hi Marine the brainmask is just a rough estimate of what is brain and what is not. You don't need to worry if it is not accurate *unless* the lh.pial and/or rh.pial surfaces end up not being accurate because of dura left in the brainmask. cheers Bruce On Wed, 21 Jun 2017, Lisa Delalande wrot

Re: [Freesurfer] Segmentation fault (core dumped) error

2017-05-29 Thread Jens Offenbach
to the files listed in the folder "mri". Maybe the problem is caused here? I will try to rerun the recon-all analysis of this subject. Thank you very much for your help! Regards, Jens   Gesendet: Montag, 29. Mai 2017 um 16:32 Uhr Von: "Bruce Fischl" An: "Freesurfer

Re: [Freesurfer] Segmentation fault (core dumped) error

2017-05-29 Thread Bruce Fischl
matic section. I will report, if the issue appears there, too. Regards, Jens   Gesendet: Montag, 29. Mai 2017 um 07:41 Uhr Von: "Jens Offenbach" An: freesurfer@nmr.mgh.harvard.edu Cc: "Freesurfer support list" Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error I

Re: [Freesurfer] Segmentation fault (core dumped) error

2017-05-28 Thread Jens Offenbach
An: freesurfer@nmr.mgh.harvard.edu Cc: "Freesurfer support list" Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error I am facing a similar issue with recon-all in FreeSurfer 6.0.0. on two subjects from OASIS-Brains. I will retry the run. This is the last log entry: mri_cc -aseg

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