Re: [Freesurfer] major lobes

Hi Doug, I recently saw your solution to a reported problem with grabbing StrictLobes WM & GM (posted on the Freesurfer forum 12/04/2013; thread title= major lobes). I have successfully grabbed the StrictLobes WM, but I am having trouble with the GM. According to the forum (posted 12/04/2013),

Re: [Freesurfer] major lobes

CentOs 6 running FS v 5.1.0. on the workstation where we have processed about 300 datasets. Many Thanks! Jenifer -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 24, 2014 2:44 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] wmparc 2 wmsurf

I'm running FSv5.1.0 on RHEL6. 1) My goal is to run a glm-fit on White Matter aparc regions for a "between group" surf-based analysis and evaluate spatial maps of significant differences. 2) I noticed that fsaverage does not have a wmparc.mgz file, so I'm currently working with bert

[Freesurfer] Matlab 2016b and localGI

Hi, Hope someone can identify my user error...I've listed below key bits of info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat startup.m). Really appreciate someone taking a look and walking me through a solution to my error? Many Thanks! Jenifer 1) Running Freesurf

[Freesurfer] Unusual hires T1 specs

External Email - Use Caution I offered to help a colleague with some Freesurfer analyses, but when I looked at the data they were processing, I found: 1) highly anisotropic voxdims 2) sub-mm in-plane resolution Data were acquired on a 3T Siemens Tim Trio. I don't think they were t

[Freesurfer] glibc error: newly formatted license file?

External Email - Use Caution Recently our cluster underwent a major upgrade...which broke my well-established Freesurfer v 6.0.0 recon-all pipeline. 1) Error message from recon-all: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mri/rawavg.mgz...

[Freesurfer] Now Hiring: Postdoc

We have a current opening for a post-doctoral associate in the areas of *image analysis* (structural and functional) and *developmental neuroscience*. Available resources include a research-dedicated 3.0T MRI scanner and analysis platforms based in MATLAB/UNIX. The successful candidate will be e

[Freesurfer] LGI error in make_outer_surface at 31

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined fun

[Freesurfer] LGI error in make_outer_surface at 31

Looks like my image processing toolbox from matlab was not properly installed. Now that I have re-installed the image processing toolbox, LGI appears to be working fine. Cheers, Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ___ Freesurfer mailing list Fre

[Freesurfer] FreeSurferColorLUT & aparc

Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off? 1) In the aparc+aseg.mgz file, intensity values for the cortical labels range from -32768 to 654, with negative values falling in some regions in the left hemisphe

RE: [Freesurfer] FreeSurferColorLUT & aparc

I'm able to view the intensity values in FSL. Is there another approach I can take to doublecheck? Jenifer -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subjec

RE: [Freesurfer] FreeSurferColorLUT & aparc

yes, the correct Sgmtn label is displayed in the TkMedit Tools -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:30 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurferColorLUT & aparc if

[Freesurfer] qdec patch

Nick, Just in case you're taking a head count, I would benefit from a patch for qdec which reads ?h.pial_lgi files as mentioned in response to Martin's posting yesterday. Cheers, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

[Freesurfer] Configure thresholds in overlay options

Hi, Running FSv405 on RHEL5. Is any descriptive information available for threshold options in the configure overlay display gui? Specifically the bases for linear, linear opaque, and piecewise thresholds? Visually, the three options appear dramatically different. Are there specific datatypes ea

[Freesurfer] qdec X error of failed request

Hi, Running FSv405 on RHEL5. Recently obtained new error when qdec was attempted. Have successfully run qdec before on this box using FSv405. Only update made was to upgrade to FSLv412. Same error persists after restarting X. Both tkmedit and tksurfer work fine. Any ideas how to fix? Many Thanks,

RE: [Freesurfer] qdec X error of failed request

Perfect fix! Thanks so much... Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] MEMPR sequence for freesurfer analyses

Has anyone attempted an MEMPR-like sequence as described by van der Kouwe et al (2008 NeuroImage 40: 559-569) on a 3T Philips Intera? The paper utilized a 3T Siemens TRIO. Are the published sequence parameters directly transferable to a 3T Philips Intera with an 8 channel head coil and SENSE? Or i

[Freesurfer] template deformation error: global region empty

Just wondering if there are any suggestions for finding a work-around when the "global region of the brain empty" error message appears after executing the following command: recon-all -autorecon1 -s CIP_H0519_ERR -notal-check. The T1 image (001.mgz) looks fine. The -notal-check flag was added o

RE: [Freesurfer] template deformation error: global region empty

Hi Bruce, I forgot to ask that question! You're right on target with identifying the problem. Many Thanks, Jenifer -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Fri 1/16/2009 1:33 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subjec

[Freesurfer] qdec & ?h.sulc

Hi, Looking for a little clarification. Using qdec to look at group differences in the surface measure ?h.sulc. Large positive values in ?h.sulc indicate greater sulcal depth, right? Large negative values in ?h.sulc indicate something about gyri? Small negative values in ?h.sulc indicate transitio

[Freesurfer] qdec & ?h.sulc

Thanks for the slide, Nick. Just a follow-up question... So does the info in ?h.sulc contain sulcal depth information wrt the mean cortical surface? How does this differ from the positive values contained in the ?h.curv file? Sorry for the confusion, but the wiki suggests that they are diffe

[Freesurfer] sulc & curv

Rudolph, many thanks for the additional details. Just a follow-up question (or two): 1. Short stubby gyri might have the following morphometric properties? a) Short feature: shallow sulcal depths would be expected to have sulc values hovering around the mean surface (e.g. around 0) in

[Freesurfer] adding uncached variable to qdec

Hi, Running FSv4.2.0 on RHEL4. I'd like to add a variable such as lgi to qdec analyses. I created a .Qdecrc and .fsgd file, ran the lgi files through mris_preproc & mri_surf2surf (following instructions for Uncached Data posted under Group Analysis of the FsTutorial). While the output of mri_gl

[Freesurfer] graph average ROI

Hi, I'm running fsv420 on RHEL4. Within the qdec module (v1.2) menu options, View, Graph the ROI --> generates average +/- SD or SE? Many Thanks, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

[Freesurfer] scale axis range

Hi, Running fsv4.2.0 on RHEL4. Within qdec, the "graph average ROI" provides valuable information in scatterplot format. Is it possible for users to define the axis range (especially the Y-axis)? For some unknown reason, we have encountered several instances where data points are not displayed s

[Freesurfer] spherical template: CMA training set

Is any information about the manually-parcellated (CMA) training set used to create the spherical template used in fsv4.*? The information reported in Cerebral Cortex (2004) 14(1):11-22 reports 36 MRI volumes from an ongoing study. Does this sound about right? Or have there been any updates to t

RE: [Freesurfer] spherical template: CMA training set

Ah...Excellent! Thanks so much for clearing things up for me. Cheers, Jenifer -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 22, 2009 11:55 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spherical

[Freesurfer] map label to subjects

Hi, I'm running fsv405 on a 64bit Linux centos5. I have not had much success with using the File - Save Label - Filename within qdec (v1.1). The gui prompt has a default filename set to lh.untitled.label and I am unable to edit that name, but I can write the default filename to the default dir (

[Freesurfer] POSTDOC POSITION OPEN

Subject: POSTDOCTORAL POSITION - structure & function of fronto-cerebellar circuits in neurodevelopmental disorders Applications are invited for an immediate postdoctoral opening in the Department of Psychology at the University of Houston, Houston TX. The position is full-time for 1 year, wi

[Freesurfer] ICV for incomplete whole brain coverage

A colleague asked me to look at some T1s for possible Freesurfer analyses. Unfortunately, several subjects do not have whole brain acquisitions (I know, quite unexpected and disappointing). Would it be possible to correct volumes of subcortical structures (which are covered by the acquisition) f

[Freesurfer] Head Points data files

Hi, What are the file format requirements for the 2 files called to load head points - *.hpts and *.trans into tkmedit or tksurfer?   We have a whole-head neuromagnetometer (4-D Neuroimaging 3600 Magnes MEG system) with 248 sensor channels. I’d like to co-register my dipole locations wi

[Freesurfer] 64bit centos utilities: mris_wm_volume & mris_volume

Recently (7 Feb 2007) mris_wm_volume for 32bit centos was posted in /pub/dist. Is there any possibility of posting 64bit centos versions of mris_wm_volume & mris_volume? I'm running Freesurfer 3.0.4 Many Thanks, Jenifer ___ Freesurfer mailin

[Freesurfer] %GM, %WM, %CSF wrt ICV - including cerebellum

I'd like to compute %GM, %WM, %CSF wrt ICV (eTIV)...including cerebellum gray/white. Are the values returned by mris_wm_volume and mris_volume for cortical surfaces only (excluding cerebellum)? So, in this case... 1) are the values in aseg.stats appropriate for both cerebral and cerebellar fra

[Freesurfer] TBV fractions: aseg

I'm using the aseg file located in /freesurfer/subjects//stats folder to calculate Total Brain Volume Fractions of GM, WM, and CSF. Within the aseg file, several csf compartments are listed, including: Left-Lateral-Ventricle (segid 4) Left-Inf-Lateral-Ventricle (segid 5) 3rd-Ventricle (segid

[Freesurfer] binary masks: 1 output file per aseg label

I'm interested in parsing aseg.mgz into separate binary mask files for each aseg label. Is this possible? The closest topic I found was located at the following URL: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu nctionalSpace 2.0 Creating binary masks The segmenta

[Freesurfer] Simple_Surface_labels2005.txt

I'd like to identify the voxel locations of each vertex within each aparc label. I found the command "mri_annotation2label" and thought it might do the trick. However, I noticed that the examples http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fannotation2label?action=h ighlight&value=mri_annotation2

[Freesurfer] XYZ coordinates of vertices within aparc labels

I'd like to retrieve information wrt XYZ coordinates of vertices within aparc labels. I have tried the following command: [] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s A total of 57 labels are returned (expecti

RE: [Freesurfer] XYZ coordinates of vertices within aparc labels

aparc label back to the scanner XYZ coordinates. Is this possible? Jenifer -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of ver

RE: [Freesurfer] XYZ coordinates of vertices within aparc labels

ually scanner coordinates.) Any suggestions how to access this information? From the help pages, I thought mri_annotation2label would do the trick... Jenifer -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, October 01, 2007 1:05 PM To: Bruce Fischl Cc: Juranek, Je

RE: [Freesurfer] XYZ coordinates of vertices within aparc labels

: Monday, October 01, 2007 1:20 PM To: Juranek, Jenifer Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels use mri_annotation2label to create a text label file for each annotation. These have the surface xyz in them. doug Juranek

[Freesurfer] xtra advice: /usr/local/freesurfer/fsl

I'm considering downloading and installing fsl_v402 (centos4, 64 bit) I currently have a stable freesurfer_v401 and MNE _v252 on the same workstation. Should the destination directory of the fsl package overwrite the existing directory: /usr/local/freesurfer/fsl Or should I maintain separat

[Freesurfer] CC q's

Hi, I'm running FSv4.0.1 on a 64bit linux platform and had a few questions about the new added feature wrt the corpus callosum segmentation added as early as v4.0.0...details were not readily returned in Wiki searches...so please point me in the correct direction? 1) The 5 separate regions of

[Freesurfer] LGI: EXITS with ERRORS

I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted). While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties

RE: [Freesurfer] LGI: EXITS with ERRORS

[mailto:[EMAIL PROTECTED] Sent: Sat 4/19/2008 7:44 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LGI: EXITS with ERRORS Jenifer, Have you installed Matlab on your computer? As far as I see it, either you don't have matlab, or the path to matlab is no

[Freesurfer] lh.aparc.a2005s: S_subcentral_ant label

We recently started playing with the ?h.aparc.a2005s annotation files (fsv401). We noticed that in /freesurfer/subject/bert, the S_subcentral_ant label is not listed as a variable in the /stats/lh.aparc.a2005s output file. However, this variable name does *sometimes* appear in some of our study s

[Freesurfer] talairach_avi

Just curious... 1) was talairach_avi (or more specifically, 4dfp suite) introduced with any particular version# of freesurfer? Or has it always been the default? 2) Any comments on differences/similarities with mritotal as called by the -use-mritotal flag within freesurfer? Many Thanks, Jenife

[Freesurfer] atlas renormalization

Another curious question: The atlas renormalization process described by Han & Fischl (2007)...which version of freesurfer was this introduced? Many Thanks, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

[Freesurfer] tksurfer display broken

Hi, I recently encountered a problem with tksurfer display (worked perfectly fine a couple of weeks ago). The only change I've made to my linux (centOs 5) system is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun process since the MATLAB 2008a install required depreca

[Freesurfer] tksurfer display broken: "smart" over-ride?

Krish & Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a "smart" window pops up reporting that "a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed". I

RE: [Freesurfer] tksurfer display broken: "smart" over-ride?

Section EndSection Section "Extensions" Option "Composite" "Disable" EndSection -Original Message- From: Paul Raines [mailto:[EMAIL PROTECTED] Sent: Wed 5/28/2008 10:10 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

[Freesurfer] tksurfer display broken: post re-install nvidia 9746

I re-installed the dell-nvidia driver (original with system). Some new behavior observed with bert: tksurfer bert lh pial yields a complete "bert" window (entire pial surface is displayed). However, the lower window "TkSurfer Tools" is not visible. Also, tkmedit bert norm.mgz fails to launch a di

[Freesurfer] tksurfer display broken: fixed

Not exactly sure how or what happened...but did manage to "fix" my tksurfer display problem. Since others on the list had reported similar problems, I thought I'd post what I did to "fix" the problem. Since I'm not a Linux guru, my "fix" is probably just a "bandaid"...but it did work...and hope

[Freesurfer] SELinux AVC denial: Matlab

While trying to check if -lgi will run on bert (on RHEL5,fsv404 and matlab r2008a), I received the following message from SELinux (please see summary below): Sorry to be so cautious, but do I change to allow_execheap boolean? The system-wide impact statement makes me a little nervous... Many

[Freesurfer] atlas renormalization

The atlas renormalization process described by Han & Fischl (2007)...which version of freesurfer was this introduced? Many Thanks, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre

[Freesurfer] seg edits

Running Freesurfer v4.0.5 on RHEL5 linux system. General Question: after using the "Edit Segmentation" tool and saving edits by overwriting the aseg.mgz file generated during $recon-all -autorecon-all...which command should I pass to re-enter the analysis pipeline at the most appropriate spot?

[Freesurfer] major lobes of cerebellum

Is there any interest in parcellation of the cerebellum into its major regions: corpus medullare, anterior, superior-posterior, inferior-posterior regions? Any easy approaches available for testing out? Would a volume-based approach be sufficient, or would a surface-based approach be necessary?

[Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow

Hi, Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command prompt. While the splash screen did appear with the inflated brain surface, the qdec interface did not appear (even after 10min). When I tried to CTRL-C the terminal window, the following error message appeared: [EMAIL

RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow

- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Wed 7/23/2008 3:47 PM To: Juranek, Jenifer Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow Jenifer, Is this new to v405, or have prior versions also had this problem? Are you running directly

RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow

dSection Any other sections of the xorg.conf file I should check? Is there a particular screen resolution I should check under Section "Screen" Options or Modes? Thanks, Jenifer -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Wed 7/23/2008 4:04 PM

[Freesurfer] Hippo-Amyg defs

Hi, Is any documentation available for describing the anatomical landmarks for demarcation of amygdala and hippocampus used by aseg? Many Thanks, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] Floating exception (core dumped)

Hi, Running fsv405 on RHEL4 (64bit) and have encountered the following error after executing recon-all -all: Floating exception (core dumped). Did not encounter this error using fsv401 on the same box. See below for the standard output to screen. Any ideas? Many Thanks, Jenifer [EMAIL PROTECT

[Freesurfer] choroid plexus

Hi, Would like to sum all CSF compartments to get a global CSF volume for each subject. Should Choroid plexus (L & R) be included in the summation? I have not seen other "non-freesurfer" apps tease out the choroid plexus. So far, I have the following 8 compartments: [Left-Lateral-Ventricle

[Freesurfer] WM intensity < CSF intensity?

Hi, I'm running fsv405 on RHEL5. I received the following message and reviewed the input images, but could not spot the problem. Any suggestions about where I should be looking in the T1.mgz? Many Thanks, Jenifer White matter intensity 0 is lower than CSF intensity 14. Please examine input imag

RE: [Freesurfer] WM intensity < CSF intensity?

Yes, in the T1.mgz, the WM is around 110 in the slices I sampled across the ant-post extent of the brain. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, September 03, 2008 11:41 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re

RE: [Freesurfer] WM intensity < CSF intensity?

Thanks, Bruce. The file upload to your server just finished. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, September 03, 2008 12:34 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WM intensity < CSF intensity? h

[Freesurfer] Freesurfer statement

External Email - Use Caution I pledge to do better. I pledge to pursue systemic change as passionately as I pursue research questions. Thank you Freesurfer Team for speaking up so eloquently with your signed statement. Jenifer Juranek __

[Freesurfer] heterotopias

Any suggestions from anyone wrt handling heterotopias? Is it best to use a custom labelname to label them as such? Current labelname="WM-hypointensities". Cheers, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.ha

Re: [Freesurfer] heterotopias

Excellent. Many Thanks! Jenifer -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, June 28, 2010 3:16 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] heterotopias Hi Jenifer, what does "handle" mean?

[Freesurfer] Gyrification index group differences

Hi Nathan, Check out this previous posting wrt using Qdec to visualize group maps (or group diff maps) based on pial_lgi data. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09281.html Cheers, Jenifer ___ Freesurfer mailing list Freesurf

[Freesurfer] -legacy

I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't look like a legacy analysis (see below). [jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001 ERROR: you have specified -legacy,

Re: [Freesurfer] -legacy

-Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Wednesday, September 22, 2010 6:51 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -legacy yes, the -legacy flag was only necessary for the v3.0 to v4.0 transition. v4.0 data

[Freesurfer] dura flag in fsv5.0.0

Since the -dura flag is not recognized in FSv5.0.0, how should mempr data (4 echoes) be passed to the latest version of FS? Many Thanks, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

[Freesurfer] MCSRCH error

While processing a normal brain through fsv5.0.0, an unfamiliar message popped up in the screen output (see below). Any ideas what I should do about this message (anything in particular I should check)? Many Thanks, Jenifer IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERR

[Freesurfer] mri_normalize

I'm running a normal brain through FSv5.0.0 using the -cw256 flag and encounter a problem at the mri_normalize stage. The nu.mgz file looks fine...WM regions have intensity values >110; cortical GM regions have intensity values 70-106; csf intensity values are around 60. The output file (T1.mgz)