Re: [Freesurfer] I need to a pass code

see a link to the file. Thanks in advance. Best! Ariel Miquelini. El vie, 8 jul 2022 a las 11:53, Jiu Chen () escribió: > External Email - Use Caution > > *Dear freesurfer,* > *I need to a pass code to expand the archive:* > > FS_7_2_0_Ubuntu_18_04_06.ova.7z >

[Freesurfer] I need to a pass code (FS_7_2_0_Ubuntu_18_04_06.ova.7z)

External Email - Use Caution Dear freesurfer, I need to a pass code to expand the archive: FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you. If you have any questions, please don't hesitate to contact me. Best! Yours, Jiu Chen, PhD Associate professor NBH and NDU E-mail:

[Freesurfer] I need to a pass code

External Email - Use Caution Dear freesurfer, I need to a pass code to expand the archive: FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you. If you have any questions, please don't hesitate to contact me. Best! Yours, Jiu Chen, PhD Associate professor NBH and NDU E-mail:

Re: [Freesurfer] I cannot start my first subject.

14, 2022 7:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] I cannot start my first subject. External Email - Use Caution Good morning I installed Oracle VM virtual box i am able to work on the tutorial patient bert but when I copied dicom file of a patient I could not work

Re: [Freesurfer] I cannot edit white matter mask

External Email - Use Caution Hi Douglas, Thank you for your reply. I mean that the voxels do not change the color value 255. Is like nothing is happening to them. What do you mean by if the surfaces are not following the gray white boundary. It is not used for anything else? If t

Re: [Freesurfer] I cannot edit white matter mask

If it works for others, then I don't know what could be going wrong. Also, it is unclear what you mean by not being able to edit it (permission? voxels don't change). Also note that you only need  to change the wm.mgz if the surfaces are not following the gray white boundary. It is not used for

[Freesurfer] I

External Email - Use Caution In Get Outlook for iOyiS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] I have a question for subthalamic nucleus ROI.

Hi Gwang-Won sorry, the STN is high on our to-do list, but we don't have anything distributable yet. cheers Bruce On Fri, 30 Aug 2019, Gwang-Won Kim wrote: External Email - Use Caution   Hi there,   I would like to make a ROI for subthalamic nucleus. But, there is not l

[Freesurfer] I have a question for subthalamic nucleus ROI.

External Email - Use Caution  Hi there,   I would like to make a ROI for subthalamic nucleus. But, there is not label name for subthalamic nucleus in FreeSurferColorLUT. How do I make a ROI for subthalamic nucleus in T1 image?   Thank you. Gwang-Won __

Re: [Freesurfer] I got a problem with open Freeview via X

External Email - Use Caution Did you use the Ubuntu package manager tools to install X and also a driver for the graphics card?   It may not work to download a driver from the NVIDIA web site depending upon what is on your machine - or if it is not supported. For X install you co

Re: [Freesurfer] I got a problem with open Freeview via X

External Email - Use Caution When I try to execute commands "glxgears" or "glxinfo", I got similar error message. Both of error message says same messages. X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 149 (

Re: [Freesurfer] I got a problem with open Freeview via X

External Email - Use Caution I'm quite sure that this is a general problem with your graphics setup that is unrelated to FreeSurfer. Can you run other software that uses your graphics card (e.g., does running glxgears produce load on your nvidia GPU), and could you post the outp

[Freesurfer] I got a problem with open Freeview via X

External Email - Use Caution I installed ubuntu 18.04.3 in my new server and also installed Freesurfer. In this server, I have two graphic cards which are RTX 2080 ti. First, I tried to open Freeview without graphic driver, it is failed. So I install the graphic driver. NVIDIA 4

[Freesurfer] I have a question for "matlabruntime"

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version(freesurfer-linux-centos6_x86_64-dev.tar.gz).The OS of my notebook CentOS (6.10).MATLAB --> /usr/local/MATLAB/R2017bMRCv84 --> /usr/local/frees

[Freesurfer] I have a question for "matlabruntime"

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version(freesurfer-linux-centos6_x86_64-dev.tar.gz).The OS of my notebook CentOS (6.10).MATLAB --> /usr/local/MATLAB/R2017bMRCv84 --> /usr/local/frees

Re: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."

Kim Reply-To: Freesurfer support list Date: Friday, 21 June 2019 at 15:25 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] I have a question for "Segmentation of thalamic nuclei." External Email - Use Caution Dear there, I tried to process “Segmentatio

[Freesurfer] I have a question for "Segmentation of thalamic nuclei."

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version.I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR]”.In two computer, there were massages “segmentThamicNuclei.sh: Command not found”

[Freesurfer] I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels) but converges only on 30 %

External Email - Use Caution Dear FreeSurfer experts, I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels). I adapted the code a little bit to accommodate the data format. I have a longitudinal design with 3 time points and

[Freesurfer] I: Demeaning of "group" covariate in LME models

Dear Doug this is a snapshot of the website (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) where the categorical variable "group" is coded as a number (see point 4) ** Example data an

Re: [Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

Thanks again Douglas! Your time and help is greatly appreciated! Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Thursday, August 25, 2016 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] I

Re: [Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

MRIwrite() writes out the image as a float, whereas FS insists that it be UCHAR or INT. To get this, run mri_convert aseg.mgz -odt int --no_scale 1 aseg.mgz View aseg.mgz to make sure it looks right, then rerun recon-all -autorecon2-cp -autorecon3 On 08/24/2016 05:51 PM, Silas wrote: > > Dear

[Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when runn

Re: [Freesurfer] I: FS-FAST bandpass filtering

Not by default, look at mkanalysis-sess -help for more details, especially the -hpc and -lpc options. Hi, I'm wondering whether the FS-FAST performed bandpass filtering. Stefano On 04/01/2016 03:11 AM, std...@virgilio.it wrote: > > > > ___ > Freesur

[Freesurfer] I: FS-FAST bandpass filtering

--- Begin Message --- Hi,I'm wondering whether the FS-FAST performed bandpass filtering. Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is in

Re: [Freesurfer] I: I: R: R: R: Re: To use a ROI.label as seed in FS-FAST

Why would the sig in MNI space overlap the native functional space? Please also look the file attached. This the sig.nii.gz (subcortical, MNI) overlapped on f.nii. Messaggio originale Da: std...@virgilio.it Data: 12-feb-2016 17.16 A: Ogg: [Freesurfer] R: R: Re: To

Re: [Freesurfer] I got error building with Read-only source.

PM, Jiho Yeom wrote: > Dear all. > > Hi. I am new to FreeSurfer. > > I am trying to build Read-only source. > > I followed the instructions in these pages: > https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS > > https://surfer.nmr.mgh.harvard.edu/fswiki/free

[Freesurfer] I got error building with Read-only source.

Dear all. Hi. I am new to FreeSurfer. I am trying to build Read-only source. I followed the instructions in these pages: https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page However I got these error messages

[Freesurfer] I got ERROR during recon-all

I'm new on FREESURFER and have tried to run recon-all refer to https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Practicedata.26commands However, I got an ERROR .. could you tell me how to run it. Last login: Mon Nov 3 23:53:19 on ttys000 freesurfer-Darwin-lion-stable-pub-v5.3.

Re: [Freesurfer] I want to know a simple thing in tksurfer

Hi Seulgi you can specify the fthresh and and slope on the command line using: tksurfer ... -fthresh -fslope or alternatively, both the min and max using tksurfer ... -fminmax where is the value at which the color saturates. Or you can set the thresholds based on rank ordering of the val

[Freesurfer] I want to know a simple thing in tksurfer

I'm using 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0' and I have a problem. I used a command 'tksurfer fsaverage lh inflated -ov surfdata' on teminal. Then, I used 'configure overlay display' in veiw>configure>overlay to set proper threshold. I could set approximate threshold values easi

[Freesurfer] I: hippocampal subfield segmentation

hello carolina to me it took about 5-6 hours. greets,   lorenzo         Da: Carolina Valencia A: Freesurfer Mailing List Inviato: Giovedì 30 Agosto 2012 20:37 Oggetto: [Freesurfer] hippocampal subfield segmentation Hi Freesurfer community,  A quick question,

Re: [Freesurfer] I had a Computer Failure, how can I resume recon-all for base (longitudinal processing)

Hi Natacha, make-all does not work for base and long. The easiest is to delete the base (unless you made edits of course), and rerun the base from scratch. You can also look at scripts/recon-all.log and see where it stopped, then use flags like -autorecon2 -autorecon3 (or more fine steps) to star

[Freesurfer] I had a Computer Failure, how can I resume recon-all for base (longitudinal processing)

Hello, I know that we can resume a recon-all command, if it's a cross-sectionnally process. In this case the command is: recon-all -make all -s subject But I had a power failure during a longitudinal study, when I try to execute : recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'O

Re: [Freesurfer] I/O performance mitigation

Mehul, to get our discussion back on the list (as inevitably other cluster users will probably bump into this same problem), the solution another user found was to modify the MNI N3 source in the following manner, quoted within bars: two modifications to the N3 distribution. first,

Re: [Freesurfer] I/O performance mitigation

Thanks for letting me know. On my side, my first guess is for some reason memory is not being allocated correctly by the the script I use (this mostly uses standard sun grid engine flags) I am trying to verify this with sysadmins. Just fyi. I am using the cluster on www.teragrid.org and one of th

Re: [Freesurfer] I/O performance mitigation

Hi Mehul, we don't sorry. We are trying to replicate it here. The fact that it's in an MNI tool and not one of our's makes it harder to track down. The delay between jobs for us is driven by how robust and rapid your storage is. Certainly a minute or two should be enough I would think, altough

Re: [Freesurfer] I/O performance mitigation

Hi Bruce and others, My question is related to the staggering of FS jobs (see thread below). Could you tell me by how much time you stagger the freesurfer on a cluster ? I am using FS 5.1 on a cluster which uses sun grid engine and I have the following error when I try to submit a large number of

[Freesurfer] I: I: Re: (no subject)

I've founded the answer at the second question. Please, tell me if my first sentence is ok. --- Dom 13/3/11, Angela Cosentino ha scritto: Da: Angela Cosentino Oggetto: [Freesurfer] I: Re: (no subject) A: fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Data: Domenica 13

[Freesurfer] I: Re: (no subject)

Sorry. The 2 lines are red and yellow. But probably nothing changes. Sorry again! --- Dom 13/3/11, Angela Cosentino ha scritto: Da: Angela Cosentino Oggetto: Re: [Freesurfer] (no subject) A: "Bruce Fischl" Cc: freesurfer@nmr.mgh.harvard.edu Data: Domenica 13 marzo 2011, 07:49 In this way, I s

Re: [Freesurfer] I/O performance mitigation

Hi David, I'm surprised you didn't have to do this in the past. We always space our jobs out. Glad there's an easy workaround cheers Bruce On Fri, 3 Sep 2010, David Mischel wrote: > We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all > jobs. The attached Word doc (I don

[Freesurfer] I/O performance mitigation

We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all jobs. The attached Word doc (I don't know how to contribute this information other than attaching the image and text using Word) shows a load graph on our file server. When 20 FS jobs began at once (all processing servers u

Re: [Freesurfer] I cannot get tutorial data

Sorry, try it now. doug wrote: Hi, Mr. and Mrs I want Tutorial file of fsfast. But I didin't get it from the following pass. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast-tutorial/fsfast-tutorial.subjects.tar.gz If you know about that please let me know. Thank y

[Freesurfer] I cannot get tutorial data

Hi, Mr. and Mrs I want Tutorial file of fsfast. But I didin't get it from the following pass. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast-tutorial/fsfast-tutorial.subjects.tar.gz If you know about that please let me know. Thank you for your help. Best regards, Kenta ___

Re: [Freesurfer] I have one question!

Zhang, I think you will need to try upgrading your graphics driver. This sort of thing happens with NVidia graphics cards. Nick On Mon, 2007-01-15 at 17:22 +0800, zhang yi wrote: > Hi, >When I was using freesurfer I met one problem: After I installed > freesurfer, I entered th