[Freesurfer] mri_convert segfault error

On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting >>ls brain* > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz > > mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii > > $Id: mri_convert.c,v 1.179.2

Re: [Freesurfer] mri_convert segfault error

Hi Doug, Yes the quoted lines were output fromt her terminal. ls -l brain.mgz > -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz > I have many Tb of disk space. I can chmod 777 the files and still seg faults. Thanks Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Ins

Re: [Freesurfer] mri_convert segfault error

I had replaced the user name in the output I posted to the listserv for security reasons. I am not on a virtual machine. Fresh install on bare metal. ls -l ../ ... > drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri > ... > > - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institut

Re: [Freesurfer] mri_convert segfault error

I do note that I can enter "freeview ./brain.mgz" and the image opens. Then I can manuall save it as a .nii - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee wrote: > I had replaced

Re: [Freesurfer] mri_convert segfault error

Perhaps something to do with libcrypt-2.*.so ?? https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee wrote: > I

Re: [Freesurfer] mri_convert segfault error

reading from ./brain.mgz...Segmentation fault (core dumped)* - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 12:44 PM, dgw wrote: > If you must use 5.1 (I would recommend upgrading), then try what Zeke > sugges

Re: [Freesurfer] mri_convert segfault error

5.1? Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 1:13 PM, Joshua Lee wrote: > Unfortunately this does not seem to work. > > locate libcrypt-2 > > > */lib/x86_64-linux-gnu/libcrypt-2.23.so

Re: [Freesurfer] mri_convert segfault error

Installing the latest version of FreeSurfer has resolved this problem. So as long as the post-processing tools are compatible with these data then I should be fine. Thanks. Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun

[Freesurfer] qdec load error missing BLT

When loading qdec I get can't find package BLT FsgdfPlot::InitFsgdf: Couldn't find fsgdfPlot.tcl on Ubuntu with FreeSurfer5.3 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] qdec load error missing BLT

tkcon.tcl fs-make.tclscuba_glut.tcl twocond-flat.tcl fs-views.tcl scuba.tcltwocond-masked-views.tcl histolabel.tcl setdefpatchview.tcl twocond-views.tcl mk-fieldsign.tcl solmovie-flat.tclwrappers.tcl - Joshua Lee, Ph.D. Post-Doctoral Researcher

[Freesurfer] (no subject)

lag via an expert.opts file." Are these expert options doing something similar to what was done in Lüsebrink, Wollrab, Speck, 2013 in *NeuroImage*, in which they " conforms the data to the minimum voxel size, which is equal in all directions if data with an isotropic resolution is used"

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

Hi Alan, Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x 0.4 mm in-plane resolution). The thickness of a CA subfield typically range between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter resolutions. Further, subfield segmentation typically requires high-cont

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

Thanks for the clarification Eugenio. Would saying that it relies on shape instead of surface be more accurate? I would like to understand better. Also, it is good news that there are plans to model the SLRM. Josh - Joshua Lee Doctoral Candidate Department of Psychology & Center for Mind

[Freesurfer] advice in registering a binary mask to Freesurfer space.

Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image.

Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.

ri_label2vol to convert the mask into FS conformed space > (assuming that that is what you want to do). > doug > > On 03/22/2013 04:43 PM, Joshua Lee wrote: > > Hi All, > > > > I wanted to get peoples advice on the best method of > > registration/interpolation t

Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.

Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student

Re: [Freesurfer] advice in registering a binary mask to Freesurfer space.

atial transforms to go from orig to norm. They are in the > same space. > > cheers > Bruce > > > On Mon, 25 Mar 2013, Joshua Lee wrote: > > Hi Doug, >> >> Is a standard 12 affine registration sufficient to get a subjects >> structural >> (in a dif

[Freesurfer] subcortical segmentation

A subcortical segmentation error sometimes get Freesurfer (v 5.1) is cortical areas coming over into the hippocampus, ignoring the wm inferior and lateral to the hippocmapus (coronal). See attached png. Will adding wm control points help, or do they not inform the aseg segmentation. What is the bes

[Freesurfer] aseg.mgz altered after auto-recon2?

Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. __

Re: [Freesurfer] aseg.mgz altered after auto-recon2?

In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee wrote: > Hi All, > > Am I right in reading the dev table that if I just want the aseg.mgz, (not > the stats output), I only need to run auto-recon1 and a

Re: [Freesurfer] aseg.mgz altered after auto-recon2?

gt; cheers, > Natalie > > > On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl > wrote: > >> Hi Josh, >> >> yes, I think that's correct. >> >> Bruce >> On Thu, 28 Mar 2013, Joshua Lee wrote: >> >> > In fact, couldn't I s

[Freesurfer] advice for subcortical Freesurfer processing of 2 year old brains

The aseg has shown poor performance in my sample. Are there settings, atlases, etc, available that might improve performance? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] advice for subcortical Freesurfer processing of 2 year old brains

Looking forward to it. - Josh On Tue, Apr 2, 2013 at 11:32 AM, Lilla Zollei wrote: > > Hi Josh, > > We do not yet have a publicly available atlas for that population. We are > working on it though and will announce it as soon as it is ready. > > Lilla > > > On Tue

[Freesurfer] failures more frequent in one hemisphere

Hi All, I recently ran a number of 2-yr-old brains through Freesurfer, and overall Freesurfer did well considering the age group. However, a subset (~10%) had catastrophic failures in the left termporal lobe in which parahippocampal cortex bled over into the hippocampal region. I've since added c

[Freesurfer] hipposubfields and data

I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to

Re: [Freesurfer] hipposubfields and data

lag to change this? The algorithm is > pretty resolution-independent, and could certainly benefit from > higher-res data. > Cheers, > /Eugenio > > On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote: > > I have read that the hippo-subfield algorithm uses the aseg for > >

[Freesurfer] subfield algorithm and subject intensity differences

I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundari

Re: [Freesurfer] subfield algorithm and subject intensity differences

result in very different subfield segmentations? Josh - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Fri, Jun 7, 2013 at 12:33 PM, Bruce Fischl wrote: > Hi Josh > > it depends on intensity differences i

Re: [Freesurfer] subfield algorithm and subject intensity differences

atlas). > /E > > > > On Fri, 2013-06-07 at 12:42 -0700, Joshua Lee wrote: > > Thanks Bruce and Eugenio, > > > > Suppose I had two identical images of a subject, but in one image I > > reduced the contrast of internal lamina while leaving the rest of the &

[Freesurfer] surface stream steps

Dear Freesurfers, >From the Wiki Freesurfer surface stream follows something like: 1. Affine registration to Tal. 2. Bias correction and skull stripping 3. Classify WM 4. Cut hemisphere planes 5. Tile WM surface 6. Refine WM surface following GM-WM intensity gradients 7. Nudg

[Freesurfer] methods Q

Hi Experts, I just wanted confirm my understanding that Freesurfer does not employ multi-atlas label fusion methods. Is this correct? Thanks, Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.

Re: [Freesurfer] methods Q

tribute the manually labeled data which we don't have IRB approval for > Bruce > > > > On Thu, 13 Jun 2013, Joshua Lee wrote: > > Hi Experts, >> >> I just wanted confirm my understanding that Freesurfer does not employ >> multi-atlas label fusion method

Re: [Freesurfer] How to avoid overlaps between volume labels?

Well you could mri_binarize the three volumes, then subtract regions using fslmaths from the FSL suite. Of course this would create gaps between your formerly adjacent regions. Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of Califo

[Freesurfer] Restart from somewhere in the middle of mri_ca_register

Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

not that I have any real hope lol - Josh On Mon, Jul 16, 2012 at 1:41 PM, Joshua Lee wrote: > Is it possible/pracitcal? This is a long step, and unfortunately my > analysis computer was rebooted in the middle of this step, and I was hoping > to present the volumes tomorrow.. ouch. &

Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

ischl wrote: > no, sorry :< > > On Mon, 16 Jul 2012, Joshua Lee wrote: > > Is it possible/pracitcal? This is a long step, and unfortunately my >> analysis >> computer was rebooted in the middle of this step, and I was hoping to >> present the volumes tomorrow

Re: [Freesurfer] subcortical gray matter volumes

In my data-set I have observed that Freesurfer has a tendency to include some amygdala into the hippocampal head, despite a visible strip of alveus white-matter segregating hippocampus from amygdala in my images. Has this tendency been noticed by others? If so, has anyone found a non-manual correct

[Freesurfer] mri_convert downsample then resample shifts image upward one voxel

I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and then again back up to 1mm isotropic space. The resultant image shifted up a voxel from the original converted straght to nii.gz. This points to the resampling procedure, and not the conversion to different file format. Suggestion

Re: [Freesurfer] mri_convert downsample then resample shifts image upward one voxel

re your exact mri_convert commands? > doug > > On 08/09/2012 06:05 PM, Joshua Lee wrote: > > I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and > > then again back up to 1mm isotropic space. The resultant image shifted > > up a voxel from the original converted s

[Freesurfer] mri_convert unsupported slice timing error

Hi All, I tried to convert a high res T2 image using mri_convert and got this error message: nifti1Read(): unsupported slice timing pattern 5 Any advice? Complete message below: mri_convert DKA2921c_20120807_001_003_t2_ tse_hippo.img bb.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:

Re: [Freesurfer] mri_convert unsupported slice timing error

I started over from the .dcm and I didn't encounter the error anymore. So alls well. - Josh On Sun, Aug 19, 2012 at 11:54 PM, Joshua Lee wrote: > Hi All, > > I tried to convert a high res T2 image using mri_convert and got this > error message: > > nifti1Read(): u

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

for the next release? gratefully, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Thu, May 31, 2012 at 5:49 PM, Bruce Fischl wrote: > Hi Joshua > > sorry, I haven't found the time to

[Freesurfer] Perirhinal Cortex ....how?

Can I get thickness values for the perirhinal (posterior parahipp too maybe???) I came across http://surfer.nmr.mgh.harvard.edu/fswiki/PerirhinalArea35Labels but the labels download link isn't existent. I tried running the commands on that page anyway but of course it can't find the label... Thank

Re: [Freesurfer] Perirhinal Cortex ....how?

k can probably get you a beta > Bruce > > > > On Dec 11, 2012, at 8:25 PM, Joshua Lee wrote: > > Can I get thickness values for the perirhinal (posterior parahipp too > maybe???) > I came across > http://surfer.nmr.mgh.harvard.edu/fswiki/PerirhinalArea35Labels but the

[Freesurfer] ooops deleted fsaverage

do I need to download the whole freesurfer package again to get it? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the p

Re: [Freesurfer] Freesurfer 5.2 release date?

Thanks for all your hard work on the coming release. Is there a feature list of whats in the new release? This would be helpful in deciding to wait on a new project I'm about to start. Thanks! - Josh On Thu, Jan 3, 2013 at 5:37 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Not

Re: [Freesurfer] FW: longitudinal analysis

I dont know if this applies but I sometimes have really long run times when image quality is bad, usually from subject movement. I drop them. Josh On Fri, Jan 18, 2013 at 1:31 PM, paul horton wrote: > Hi Bruce and Martin, > > Thanks for your replies. > > With regards to the questions from Bruce,

Re: [Freesurfer] beta

Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky wrote: > Colin, > > It will still error if any dimension is greater than 256, which then means > the flag -cw256 must be added to recon-al

Re: [Freesurfer] beta

rough the standard > recon-all, then run a postprocessing surface deformation on the higher res > data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs. > > cheers > Bruce > > > > On Mon, 21 Jan 2013, Joshua Lee wrote: > > Does this mean that using F

Re: [Freesurfer] beta

On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: >> >> Message: 7 >> Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) >> From: Bruce Fischl >> Subject: Re: [Freesurfer] beta >> To: Colin Reveley >> Cc: Joshua Lee >

[Freesurfer] upsampling aseg.mgz to dimension and spacing

I would like to upsample the aseg.mgz to Dimensions: 370X512X512 Spacing 0.5mm in x,y, and z. Any suggestions? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati

Re: [Freesurfer] upsampling aseg.mgz to dimension and spacing

forgot to mention, this is to upsample Freesurfer Aseg to compare with manually traced hipp volumes from original structural images. - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Mon, Feb 4, 2013 at 11:1

Re: [Freesurfer] upsampling aseg.mgz to dimension and spacing

I do indeed. Thank you very much! - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Mon, Feb 4, 2013 at 11:19 AM, Bruce Fischl wrote: > Hi Josh > > do you have a volume with those dimensions? If so

[Freesurfer] when aseg fails

Hi All, I'm just wondering what kind of protocol people are using to address the situation when Freesurfer has a catastrophic failure in accurately segmenting the sub-cortical structures. While manual editing is an option, are there upstream changes that might improve the subcortical segmentation

[Freesurfer] dual installation question

If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh __

Re: [Freesurfer] dual installation question

etc. > and then > export FREESURFER_HOME=/freesurfer/5.1 > etc > Hth, S. > > > On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: > > Hi Josh, > > you can modify the SetUpFreeSurfer.sh to source the correct version. > > Hth, Shantanu > > > > On Th

Re: [Freesurfer] Hippocampus volume calculations

expects, would the hipposubfields algorithm do its magic on this volume? Joshua Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga < gariko...@gmail.com

[Freesurfer] 3T MPRage flags

The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences. I use 3T MPRages. What is the recommended use in this case? Thanks Josh ___ Freesurf

[Freesurfer] subcortical atlases

Hello Freesurfer Gurus, I was wondering whether the original individual subject atlases used to construct the probabilistic atlases for subcortical segmentation have been made available for download? Thanks! josh - ___ Freesurfer mailing list Freesurfer@

Re: [Freesurfer] subcortical atlases

I understand. Thank you Bruce, for you good work. Joshua - Joshua Lee Doctoral Candidate Department of Psychology & Center for Mind and Brain University of California, Davis 530.747.3805 On Wed, Jun 4, 2014 at 5:53 PM, Bruce Fischl wrote: > Hi Josh > > sorry, it was impossib

[Freesurfer] protocol question

Dear Freesurfer Experts, I am trying to better understand what regions of the hippocampal formation are meant to be included in the hippocampal label (e.g. inclusion of the alveus/fornix, lateral boundaries around the subiculum, superior boundaries in the tail, etc.). Has the protocol used to man

[Freesurfer] Hippocampal Sub-Field Segmentation -Appropriate Scan Protocol to Use

Dear Experts, I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T Siemens Trio to manually segment hippocampal subfields. However, I wonder whether the protocol is appropriate for use with the new Freesurfer subfield segmentation tool. Specifically, our hi-res scan does not ca

[Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

Are there any existing Amazon EC2 AMI registered publicly that can be used? I want to analyze a lot of data fast. Thanks, - Joshua Lee ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

I think I may have found it as a public ami with freesurfer 5.1. Testing it out on Bert right now. Thanks!! - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 2011/10/30 Joshua Lee > I think I may have found

[Freesurfer] Error During Talairach Transform

ts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 ___ Freesurfer mailing lis

Re: [Freesurfer] Error During Talairach Transform

Small Update: Error Disappears if Using Freesurfer version 5.0 instead of 5.1. However, since I am keenly interested in the hippocampal-subfield segmentation capabilities of the most recent version, I am loathe to regress to an earlier version of FreeSurfer - Joshua Lee Graduate Student Center for

Re: [Freesurfer] Hippocampal Sub-Field Segmentation

Thats an interesting suggestion, givien my recently reported issues with the talairach in FreeSurfer 5.1. - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Wed, Nov 2, 2011 at 11:41 AM, Bruce Fischl wrote:

Re: [Freesurfer] Error During Talairach Transform

Thanks Nick, Is use-mritotal equivalent to what version 5.0 does by default? Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc? - Joshua Lee Graduate Student

Re: [Freesurfer] Error During Talairach Transform

Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote: > > Thanks Nick, > > > > Is use-mritotal equivalent to what version 5.0 does by default? > > > > Also, any suggestions on why this talairach error would occur only on > > a portion of my data, despite all being collect

Re: [Freesurfer] Error During Talairach Transform

1 >> uses orig.mgz. >> >> its hard to say why it would fail for some subjects but not others, >> other than head positioning and to some degree ventricle size makes a >> difference. >> >> n. >> >> On Wed, 2011-11-02 at 16:10

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

arger disk that comes with the instance. I had disk-write errors because the the main partition ran out of space. Anyway, ec2 rocks with Freesurfer. - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 2011/11/12 Nola

Re: [Freesurfer] Freesurfer on Windows!

I'd try reinstalling virtualbox. Then I'd make sure that you adjust the vm with enough ram, videocard memory, etc. It should work fine. I run the same setup all the time, and I don't believe that this is a 'known issue'. Joshua On Mon, Nov 14, 2011 at 8:25 AM, wrote: > Hello Friends, > > I am

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

malicious intent. Moreover, it could contain such scripts as makes the analysis process easier. - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior > Ok. I'll labe

Re: [Freesurfer] Hippocampal Sub field segmentation

At least by my reading of the Duvernoy Human Hippocampus atlas, the most anterior and posterior extents of the hippocmapus (perhaps just a slice at the tips in most scans) are almost entirely composed of the CA1 subfield. Thoughts? Joshua - Joshua Lee Graduate Student Center for Mind and Brain

Re: [Freesurfer] Hippocampal Sub field segmentation

irly minor points. Still, I wouldn't mind some comments on these observations, as they were changes I have been proposing to make in the segmentation protocol used in my lab. Best, Joshua Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University o

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

on for the licensing >>> issue. >>> >>> --**--** >>> - >>> Pedro Paulo de Magalhães Oliveira Junior >>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br >>> >>

Re: [Freesurfer] Virtual Box crashes

Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding a bit more video memory to the vm. BTW, is there an error message, or does it just silently shut down? - Joshua On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V. wrote: > Dear all, > > Please help with the following pro

Re: [Freesurfer] Virtual Box crashes

> > Best, > > Veronica > > ** ** > > ** ** > -- > > *From:* nimzodisas...@gmail.com [mailto:nimzodisas...@gmail.com] *On > Behalf Of *Joshua Lee > *Sent:* maandag 21 november 2011 17:20 > *To:* Popescu, V. > *Cc:* freesurf

Re: [Freesurfer] Virtual Box crashes

size). On the host there is room enough. I tried memory > ballooning but it doesn’t work (no 64-bits host). > > Thank you! > > Best, > > Veronica > > ** ** > > ** ** > -- > > *From:* nimzodisas...@gmail.com [mailto:ni

[Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh __

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

OK, I think I can take the output of binarize and then use FSL's fslroi tool to split up on my plane, the find the volume of that final mask...that will work as long as the output of binarize is in the same space as its input.?. On Wed, Nov 23, 2011 at 8:12 AM, Joshua Lee wrote: >

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

ab, like > aseg = MRIread('aseg.mgz'); > vol = length(aseg.vol(:,:,n:256) == ID); > where ID is the code number for the ROI you want as found in > $FREESURFER_HOME/**FreeSurferColorLUT.txt > doug > > Joshua Lee wrote: > >> Hi All, >> >> I would

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

ok at particular regions, say left hipp??? Josh On Wed, Nov 30, 2011 at 1:39 PM, Bruce Fischl wrote: > probably not, as the aseg.stats calculation uses partial volume estimates. > > cheers > Bruce > > On Wed, 30 Nov 2011, Joshua Lee wrote: > > Hey Doug, THanks. That loo

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

I'm glad you caught that because I suddenly got really confused! Thank Bruce for all your hard work! Josh - On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl wrote: > oops, I meant the aseg.stats, not the aseg.mgz > > On Wed, 30 Nov 2011, Joshua Lee wrote: > > Hi Bruce, >

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

Nov 30, 2011 at 2:32 PM, Joshua Lee wrote: > I'm glad you caught that because I suddenly got really confused! Thank > Bruce for all your hard work! > Josh > - > > > On Wed, Nov 30, 2011 at 2:21 PM, Bruce Fischl > wrote: > >> oops, I meant the aseg.stats, n

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

suggests, would allow the edits I think, but then I'd have to rewrite the file from matlab.. I think. Josh On Wed, Nov 30, 2011 at 2:49 PM, Bruce Fischl wrote: > yes > > On Wed, 30 Nov 2011, Joshua Lee wrote: > > Actually, I have one last-last question. >> If I use m

Re: [Freesurfer] Computing Volume of Segmentation Label Above or Below a User-Defined Plane

Forgive me, I hadn't realize that tkmedit had a fill a function. I can do what I propsed easily. Thanks again! - Joshua On Thu, Dec 1, 2011 at 11:15 AM, Joshua Lee wrote: > Since it has be reiterated many times that aseg.stats is calulated using > estimates of partial volumes th

Re: [Freesurfer] Error: [Cannot allocate memory] having 16GB of Memory.

of memory for one recon-all process to ever reach...) To solve this, you need to get a 64 bit installation, or find a way to stop MRIalloc from needing so much memory. Best of luck Joshua - Joshua Lee Center for Mind and Brain & Department of Psychology University of California, Davis On

[Freesurfer] Entorhinal Labels and labels generally

I'm relatively new to Freesurfer, and have mostly focused of the aseg.mgz segmentation. However, I am also interested in entorhinal cortex and loaded the label up in tkmedit. What I noticed was that it seemed each label essentially noted the border between white and gray matter, but didn't really c

Re: [Freesurfer] hippocampal subfields segmentation

I am not an expert but I'll say this as far as compliance to Duvernoy: In the body of the hippocampus, compliance to Duvernoy is quite strongmuch better than any others I've seen. However, according to my reading of Duvernoy, the positions of the subfields change in the anterior head and poster

[Freesurfer] Hippocampal-subfields to ROI

Hi All, I am wanting to run a functional analysis in spm using the hippo-subfields as individual roi's. Thus I need to convert into a binary mask that is in SPM space. Knowing that the sub-field segmentations are probabilities [0..255] I chose a threshold (i.e. ~95% certainty, corresponding to a v

Re: [Freesurfer] Hippocampal subfield: average standard T1 ore use higher resolution

I think many have better scans than 1mm. Right now I'm using 0.7mm iso with decent snr, and am collecting 2 scans (about 7 min each), and on most slices I can see internal structural detail. It does seem a shame that all this detail is not used for hippo-subfield segmentation. - Joshu

[Freesurfer] Question about hippocampal-subfield probability map

Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a >50% chance (i.e. mri_binariz

Re: [Freesurfer] Question about hippocampal-subfield probability map

Ha nevermind. While true, I can just mask the masks with each other and drop the over lapped regions. - Josh On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee wrote: > Dear experts, > > The hippocampal-subfield are expressed as probability maps. For each > subfield, each voxel i

Re: [Freesurfer] Question about hippocampal-subfield probability map

That is, I can use fslmaths from fsl suite to subtract my binarized subfield rois. - Josh On Tue, Feb 14, 2012 at 4:58 PM, Joshua Lee wrote: > Ha nevermind. While true, I can just mask the masks with each other and > drop the over lapped regions. > - > Josh > > > On Tue,

[Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

ure versions of Freesurfer will limit use of the old stream to situations in which tal-check fails. Thanks you all. Sincerely, Joshua Lee ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

> > best, > > Alan > > On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee wrote: > >> Hi All, >> >> I thought I'd share my recent experiences with the newest Freesurfer v. >> 5.10 and subcortical segmentation. >> >> I ran a large sample of

Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

I was told to use this recon-all flag and my talairach problem went away: -use-mritotal - Josh On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky wrote: > Ed, > > email probably trounced it. recon-all is a text file. attached is a > gzipped version. use gunzip to unpack it. > > N. > > > > On Tue,

Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

wait it was Nick that told me to use this a while back when I had tal-check failures...I just posted about my current issues where I discuss my recent experiences with a high rate of talairach failures in the current version. - Josh On Tue, Apr 17, 2012 at 12:49 PM, Joshua Lee wrote: > I

Re: [Freesurfer] -use-mritotal

As I mentioned, this new recon-all file resolved my issue with poor hippocampal segmentations - Joshua Lee On Thu, Apr 19, 2012 at 8:51 AM, Steven Korycinski wrote: > > Hi all, > > I've been following an e-mail on this list-serve from Joshua Lee > regarding poor hippocampal se

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