[Freesurfer] patching 5.1

Hello All Several years ago Freesurfer 5.1 was patched to resolve some issues. I just remember the patch resolved issues plaguing 5.1 and earlier. how does one get the patch version. no where on the FTP server i can see patched versions and instruction on performing a patch. Aaron Tanenbaum

[Freesurfer] converting a volume to a surface

specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] converting a volume to a surface

hing wrong thank you Aaron Tanenbaum On Wed, Jul 10, 2013 at 11:34 AM, Douglas N Greve wrote: > > You will need to register your volume with the anatomical with > bbregister. bbregister will take a "template" which should be the time > point you used for motion correction.

[Freesurfer] break up time course nifti

hola freesurfers, I have a time course surface nii files. I would like to break up the time course into many nii files for each time frame. Is there an easy way of doing this. Thank you Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer

[Freesurfer] Description of a few files generated by

I would like to get a clarification on what some the the files generated by FreeSurfer recon-all based on the URL https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles The web pages says the nu.mgz "This is a intensity normalized volume generated after correcting for non-uniformity in th

[Freesurfer] Longitudinal Pipeline

I am interested in knowing what type of alignment goes into the last stage of the longitudinal pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find the warp? ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

Re: [Freesurfer] Longitudinal Pipeline

age there is a nonlinear atlas alignment that is specific to > each timepoint. We are working on building a nonlinear base, but it is not > distributed yet. > > cheers > Bruce > On Sun, 14 Jan 2018, Aaron > Tanenbaum wrote: > > > > > I am interested in knowing wh

Re: [Freesurfer] Longitudinal Pipeline

w we have some > tools around to convert to ANTS format, but I'm not sure about fnirt. I'll > cc MJ who may know (hi MJ!) > > cheers > Bruce > > > > On Mon, 15 Jan 2018, Aaron Tanenbaum wrote: > > Is the warp saved anywhere and where can I find it? Also is th

Re: [Freesurfer] Longitudinal Pipeline (fwd)

but > don't apply it (so > don't require an extra resampling). I know we have some tools around to > convert to ANTS > format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!) > > cheers > Bruce > > > On Mon, 15 Jan 2018, Aaron

[Freesurfer] Using mprage flag.

External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all? Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_ca_register

External Email - Use Caution Hello FreeSurfers, I am trying to find what the -l flag does for the program mri_ca_register program. Does not seem to be documented anywhere but i could be mistaken. Aaron Tanenbaum ___ Freesurfer mailing

[Freesurfer] crypt_gkey = (null)

External Email - Use Caution I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of

Re: [Freesurfer] crypt_gkey = (null)

; can be > an issue with FreeSurfer). > > $ cat /proc/sys/crypto/fips_enabled > > If it returns zero, it could be an issue with a system library like glibc > on CentOS 7.5 > (that does not happen on older versions of CentOS). > > Either way, this is not your doing ;-)

[Freesurfer] missing ribbon.mgz

External Email - Use Caution I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am getting an error, see below I am using the command recon-all -s BOLD-52_v1 -mprage -autorecon2 This has happened before. What did I do wrong. #@# ASeg Stats Fri Jul 13 12:55:

Re: [Freesurfer] missing ribbon.mgz

xist? > > Peace, > > Matt. > > From: on behalf of Aaron > Tanenbaum > Reply-To: Freesurfer support list > Date: Friday, July 13, 2018 at 5:24 PM > To: Freesurfer > Subject: [Freesurfer] missing ribbon.mgz > > External Email - Use Caution > > I am a

Re: [Freesurfer] missing ribbon.mgz

External Email - Use Caution I just noticed that this problem is a now and resolved. I just have to replace the mri_segstats. Thank you for your time. On Fri, Jul 13, 2018 at 6:08 PM Aaron Tanenbaum wrote: > Yes, I first ran autorecon1 and 2 for the initial processing. I t

[Freesurfer] wm.mgz values

External Email - Use Caution Hello Freesurfers. I was wondering of for the purposes of editing wm.mgz if changing voxel values to anything but 255 and 1 will be useful in anyway. If so I was wondering if you can explain to me what the following values mean and how do I use them.

[Freesurfer] updateing freesurfer.

External Email - Use Caution I tried updating freesurfer 6.0 using the command fs_update. I get the following output. > Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > >Running this will update some of your freesurfer binaries. > > Shall I proceed? [y/

Re: [Freesurfer] acquisition protocols 3T Prisma

External Email - Use Caution I suggest you talk to the folks at Washington university in St Louis. There has been considerable amount of work looking at this. You should contact the following individuals Steve Petersen s...@wustl.edu Avi Snyder azsny...@wustl.edu Michael harms

Re: [Freesurfer] acquisition protocols 3T Prisma

list, as Mike has > done a lot of work on the HCP-Style acquisition protocols. > > Matt. > > From: on behalf of Aaron > Tanenbaum > Reply-To: Freesurfer support list > Date: Friday, October 19, 2018 at 3:23 PM > To: Freesurfer > Subject: Re: [Free

[Freesurfer] Freesurfer 5.3 flags

External Email - Use Caution Hello freesurfers, Our lab has been using freesurfer 5.3 for a while. We use the following flag when we run the initial recon-all -mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon -custom-tal-atlas TRIO_PIB_NDC_as_mni_average_3

[Freesurfer] T2/Flair benefits in freesurfer 6.0

External Email - Use Caution I am not too sure if I have asked you this question before. I know the use of a flair or T2 helps with dealing with the dura. I was wondering if there are other benefits? ___ Freesurfer mailing list Freesurfer

[Freesurfer] Lesion mask

External Email - Use Caution I am working on a project where we are attempting to automate localization of white matter hyper intensities. So far it looks good. I was wondering is there a way to feeding this mask to FreeSurfer 6.0 to help improve of the parcellation and segmentati

[Freesurfer] Recon-all taking 20 hours to run.

External Email - Use Caution I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu. The super computer is about 3 years old. Of those 38 subjects, 7 exceeded 20 hour time limit on the batch script. The others took about 12 hours to finish. All subjects had a 1m

[Freesurfer] How do I get FreeSurfer to use a custom Talairach target.

External Email - Use Caution I am wondering if there is any documentation about getting FreeSurfer to use a custom Talairach target. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] T2 seq. for hippocampus ??

External Email - Use Caution Eugenio, You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but the Flair is. Is a FLAIR in general not benifisiol On Fri, May 18, 2018 at 2:02 PM Anik Dar wrote: > External Email - Use Caution > > Hi All, > > I have 1x1x3

Re: [Freesurfer] T2 seq. for hippocampus ??

, 2019 at 2:20 PM Aaron Tanenbaum wrote: > Eugenio, > You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but > the Flair is. Is a FLAIR in general not benifisiol > > On Fri, May 18, 2018 at 2:02 PM Anik Dar wrote: > >> External Email - Use Caution &g

[Freesurfer] multiple T2s

External Email - Use Caution Does freesurfer 6.0 have the ability to use multiple T2s in recon-all. If so how does one get it to work. It only seems to use the last T2 in the call to recon-all. ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] multiple T2s

External Email - Use Caution Thank you dude On Sun, Sep 8, 2019 at 9:22 AM Bruce Fischl wrote: > Hi Aaron > > you may need to motion correct and average them yourself. We'll put it on > our feature request list though > > cheers > Bruce > On Sat

[Freesurfer] freesurfer 6.0 hires fix

External Email - Use Caution I noticed that you guys released a fix to improve the -hires option. I have been processing some of our data using the hires flag. if i use this fix do i need to run recon-all from the beginning or can I run over the old folders? __

[Freesurfer] Compiling freesurfer 6.0 on centos 8.1

see what works and what does not on different versions of centos. Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Question about a feature introduced in FS 7.0

when this should be used? Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Question about a feature introduced in FS 7.0

ve any examples of when this should be used? > > Aaron Tanenbaum > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Question about a feature introduced in FS 7.0 {Disarmed}

; freeze to value 247 (FreezeSurface in > $FREESURFER_HOME/FreeSurferColorLUT.txt) > Then run recon-all with -autorecon2-surfonly -autorecon3 > > > On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote: > > External Email - Use Caution > So I never got a response for my question.

[Freesurfer] The lookuptable value of Virchow–Robin space

External Email - Use Caution Ideally, what should Virchow–Robin space be labeled as. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution Read the release notes. Can I with the new version run a recon-all over processed 7.1.1. I am interested in the ability to edit filled.mgz and applying this to 7.1.1 recons. On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve wrote: > We are please t

[Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

External Email - Use Caution What does Freesurfer do with a T2 if you do not use the t2pial flag? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

External Email - Use Caution What about for 7.1? On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve wrote: > What version are you running? In 7.2, it will automatically set the t2pial > flag when you specify -t2 > > On 9/27/2021 11:53 AM, Aaron Tan

[Freesurfer] using brain mask from older FreeSurfer version on a newer

External Email - Use Caution Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any obje

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

ust changed the freesurfer version , thnx for > your help > > Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum > a écrit : > >> External Email - Use Caution >> >> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans >> to do. I see that

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

You should be able to run 7.2 on top of the 5.3 and at will take all your > edits (make a copy of your 5.3 data first:) > > > On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote: > > External Email - Use Caution > Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands

Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

External Email - Use Caution So I believe I posted something like this a while ago. My observation is that edits removing voxel from the brain mask does not always remove inclusions for the cerebellum. It seem to work for the rest of the brain. I find this to be a common occurrence

Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

. On Wed, Jun 22, 2022, 9:23 AM Aaron Tanenbaum wrote: > So I believe I posted something like this a while ago. My observation is > that edits removing voxel from the brain mask does not always remove > inclusions for the cerebellum. It seem to work for the rest of the brain. > I find

[Freesurfer] mri_volsynth fails but exits with 0 exit status

External Email - Use Caution I am currently running FreeSurfer 7.4. I wrote a script using the program mri_volsynth. I noticed for the first time the program was trying to write files where it did not have write permissions. It outputted a few error messages but gave a 0 exit sta

[Freesurfer] Doing math on mgz file

External Email - Use Caution Is there an equivalent to fslmaths in freesurfer? Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

Re: [Freesurfer] Doing math on mgz file

urfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Aaron Tanenbaum > *Sent:* Tuesday, July 9, 2024 2:07 PM > *To:* Freesurfer > *Subject:* [Freesurfer] Doing math on mgz file > > > > *External Email - Use Cautio

[Freesurfer] making the face mask thicker mideface

External Email - Use Caution Is there a way to make the face mask generated by mideface thicker? On its own it is fine however when we need to deface a T2 there may be some motion such that the mask does not do well when registered to the T2. ___

[Freesurfer] mideface: facemask not found

External Email - Use Caution I have been writing scripts with the mideface program. Her the exact line of code i am using. mideface --i $Anatfolder/${mprs[0]}_T1w.nii.gz --odir $defacefolder --o $defacefolder/bids/${mprs[0]}_desc-defaced_T1w.nii.gz --pics --facemask facemask.mgz

Re: [Freesurfer] mideface: facemask not found

he line it did not generate the facemask.mgz file. I tracked the problem to line 310 in mideface script, It should just be removed. It resets the facemask variable to the default setting despite it being handled in the parse_arg section of the script. On Fri, Aug 9, 2024 at 2:49 PM Aaron Tanenbaum w

[Freesurfer] Operating systems

supercomputers run Redhat which worked great when you compiled with CentOS. I was wondering if you are going to consider either rocky or almalinux. Both are distributions that came out of the ashes of centos which is why I ask. Aaron Tanenbaum

[Freesurfer] FreeView feature request

External Email - Use Caution I am looking set up freesurfer to do two things. If they are not currently possible then I would like to submit two feature requests for freeview. Here they are When making voxel edits, it would be useful to see all voxels the mouse is pointing to. Cu

[Freesurfer] Change made in the release of FSL 6.0.6 may affect Freesurfer

External Email - Use Caution I have noticed a change made in the release of FSL 6.0.6 that may affect FreeSurfer. FSL executables now lie in ${FSLDIR}/share/fsl/bin not ${FSLDIR}/bin. The Freesurfer set up script adds ${FSLDIR}/bin to the PATH. Not sure if this causes any trouble.

[Freesurfer] create a mgz with one value

External Email - Use Caution Hello, I am trying to generate a mgz with identical header and dimensions as another mgz file. However I would like all voxels to be set to one value. What is the best way to do this? Thank you ___ Freesurfer

[Freesurfer] freeview: set file as read only

External Email - Use Caution Hello, Is there a way to set a loaded volume as read only in freeview on the command line? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

[Freesurfer] mri_mask error exits returns a zero exit status

External Email - Use Caution Hello, FYI, I recently noticed that mri_mask returns a zero exit status when it is unable to write the output. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] mri_mask error exits returns a zero exit status

External Email - Use Caution I should have said I am using FS 7.3 on Ubuntu 20.04 On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum < aaron.b.tanenb...@gmail.com> wrote: > Hello, > FYI, I recently noticed that mri_mask returns a zero exit status when it > is unab

[Freesurfer] FSL on recon-all

External Email - Use Caution Hello FreeSurfers, I just need to know if the FSL is used in the recon-all scripts. Basically if FSL_DIR is different will the recon-all produce different values. Thank you Aaron. ___ Freesurfer mailing list F

Re: [Freesurfer] High resolution T1

External Email - Use Caution On Mon, Jan 30, 2023 at 12:40 PM Lee, Sang Hoon wrote: > External Email - Use Caution > > Dear, Matt, > > > > What kind of issues did you have with version 7.x and the hires stream? > > It would help us to know what we are facing… > > Thanks.

[Freesurfer] Senior research position

, email will be ignored. Aaron Tanenbaum Senior Neuroimaging Engineer,ReqJR72355.docx Description: MS-Word 2007 document ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] neurological view on command line

External Email - Use Caution Is there a flag on the command line to turn on neurological view or do I have to turn it on in the GUI. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

External Email - Use Caution Hi, I saw this thread and was wondering about the details of this patch. Does this patch affect the standard recon-all call or is this meant for a special flag. Also I was also wondering what issue did it solve? Thank you. On Wed, Feb 22, 2023 at 11:52

[Freesurfer] Apply a nonlinear transform to a surface.

External Email - Use Caution I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how

Re: [Freesurfer] Apply a nonlinear transform to a surface.

Dunno if FreeSurfer offers this. > > > > Matt. > > > > *From: * on behalf of Aaron > Tanenbaum > *Reply-To: *Freesurfer support list > *Date: *Friday, March 3, 2023 at 7:26 PM > *To: *Freesurfer > *Subject: *[Freesurfer] Apply a nonlinear transform to a surfac

Re: [Freesurfer] Substantia nigra segmentation status

External Email - Use Caution Good luck. It requires a 7T to separate the compacta and reticulata. Localizing the the substantia nigra is impossible with standard MPRAGES but can be done if you modify the sequence or use a adequate T2 . There are papers that discuss how to locali

[Freesurfer] head in a bad position in scanner

External Email - Use Caution We acquired some data this morning where the participant's head was in an unusual orientation. The participant has cervical dystonia. I have processed data like this before and freesurfer always fails. I am assuming Freesurfer is unable to register the

[Freesurfer] recommended change to FreeSurferEnv.sh

External Email - Use Caution Recently FSL has changed the location of the bin directory they want you to use. The FreeSurfer setup script adds the old binary folder to the PATH not the new one. This is causing quite a bit of trouble for me. I made changes to the FreeSurferEnv.sh.

Re: [Freesurfer] ERROR: flag i unrecognized

External Email - Use Caution I noticed the "-" used for the i and all is longer than the one used for the s. It's a subtle difference and a problem if you are copying text from Windows to Linux. Just replace the long hyphen with the short one. On Sat, Apr 15, 2023 at 7:02 PM Fra

Re: [Freesurfer] FS version 8-beta

External Email - Use Caution Awesome, Will this version be able to process over older versions of FreeSurfer? On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve wrote: > Hi All, as some of you have figured out, we have a beta version of FS > 8.0.0. Please give it a spin and let us

Re: [Freesurfer] Synthstrip error in FS v. 8.0.0 beta

External Email - Use Caution Awesome, Will this version be able to process over older versions of FreeSurfer? On Wed, Nov 6, 2024 at 12:51 PM Raikes, Adam C - (adamraikes) < adamrai...@arizona.edu> wrote: > External Email - Use Caution > > Hello Developers, > > I was atte

[Freesurfer] copy headers

External Email - Use Caution Hello All, Is there a FreeSurfer tool that will copy header information from one image to the other with the same dimensions. I tried mri_copy_params but it did not change the whole header, notably fov, startz, and endz. ___