[Freesurfer] missing DOSS option in QDEC
Hi surfers, as of FreeSurfer version 5.3, i am missing the option to choose between DOSS and DODS design in QDEC. The radiobuttons in the design tab are no longer there. The default behaviour, judging from the results, seems to be DODS. Has this option been removed? regards, Andreas ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] question abt optic chaism volume
Hi All, I am using freesurfer 5.1 for my analysis. In FS 5.1, does the Supratentorial volume include the Optic chaism volume ? Please let me know. Thanks Ri ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] missing DOSS option in QDEC
Andreas, DOSS was removed from qdec because the contrast generation code in qdec was not appropriate for it (and we didnt have time to add it). You will have to use the command-line mri_glmfit and create your own contrasts to use DOSS. There are examples on the wiki i think. Nick Hi surfers, as of FreeSurfer version 5.3, i am missing the option to choose between DOSS and DODS design in QDEC. The radiobuttons in the design tab are no longer there. The default behaviour, judging from the results, seems to be DODS. Has this option been removed? regards, Andreas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ERROR: recon-all -subcortseg
Akio, You should just run -autorecon2 instead of -subcortseg in order to get the subcortical segmentation. Nick Hi Freesurfer experts, After installing v5.3.0 (CentOS 6 64bit), the command recon-all -s test -i sample-001.mgz -i sample-002.mgz -autorecon1 finished without error. Then, when I ran recon-all -s test -subcortseg, I got the following error: == $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --ctab /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test sysname Linux hostname dhcp006 machine x86_64 user yamamoto UseRobust 0 atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) MRISread(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white): could not open file == I encountered this error in v5.2.0, and am still having the same error in v5.3.0. Is this a known issue? I attached the recon-all.log file. Any help is greatly appreciated. Best, Akio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Autorecon2 missing ribbon.mgz error?
Jamie, Does running with the -all flag run all the way to complete without error? We recommend running with -all and then inspect for defects afterwards instead of running the first run in stages. Nick Hi Freesurfer List- My group just recently installed 5.3.0 and I kept running into the same error during -autorecon2 where mri_segstats could find ribbon.mgz. I was slightly stumped on the issue, as the ReconAllTable says mri_segstats isn't run until autorecon3? I attached my bugr output and also my log file for one subject (I have about 10+ subjects that error in the same way). It looks like -inflate2 finished fine (which was previously one of the last steps in autorecon2). Any thoughts? Any help is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshan...@gmail.com Homepage: http://brainimaging.waisman.wisc.edu/~hanson/ - FREESURFER_HOME: /apps/x86_64_sci6/freesurfer-latest Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Scientific Linux release 6.2 (Carbon) Kernel info: Linux 2.6.32-279.22.1.el6.x86_64 x86_64 - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] brain parenchymal fraction calculation
Hi All, I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction (GM+WM/GM+WM+ventricularCSF). In aseg.stats, I get the whole GM vol and I can also get the total ventricular CSF by adding the vols of different ventricles. But I am confused abt the terminology - CorticalWhiteMatterVol is this volume the total white matter in the brain or does this exclude something ? Please advise. Best Ri ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] brain parenchymal fraction calculation
It excludes WM in cerebellum and brain stem. doug On 05/21/2013 10:31 AM, Ritobrato Datta wrote: Hi All, I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction (GM+WM/GM+WM+ventricularCSF). In aseg.stats, I get the whole GM vol and I can also get the total ventricular CSF by adding the vols of different ventricles. But I am confused abt the terminology - CorticalWhiteMatterVol is this volume the total white matter in the brain or does this exclude something ? Please advise. Best Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to extract subjects' volume based on mask from spm?
Hi Mingxia, if you have a binarized map, then just use --id 1 with mri_cor2label (not need to for mri_binarize if it is already binary) doug On 05/21/2013 03:55 AM, zhang mingxia wrote: Hi Doug, Thanks very much. A few more question after I read the description of mri_cor2label. 1. there is a compulsory of mri_cor2label: --id (0-255). How can I find the 'labelid'? 2. If I understand correctly, the final label will be made within one particular 'labelid'. How if this mask is in more than one labels (Sorry I haven't used Freesurfer for a long time, my understanding is the labelids represent different regions. It may be wrong) ? 3. I have had the binarized mask created from spm, do I also need to use mri_binarize? Mingxia On Mon, May 20, 2013 at 6:51 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try mri_binarize followed by mri_cor2label doug On 05/20/2013 03:57 AM, zhang mingxia wrote: Dear Freesurfer experts, I analyzed functional data by spm and made a mask (analyze format). I have also run recon-all of structural data. My question is: how to extract mean volume (from structural data) of the mask(from spm)? I only extracted volume(or thickness) of ROI of a label edited by myself and annotation file. If I can convert analyze format to a label or annotation file, I can use that method. But how to convert analyze format to a label or annotation? Or is there any easy way? Thanks in advance! Mingxia Zhang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Can I mask out NaN vertices for smoothing?
you can use mris_fwhm with the mask option. Just give it a maks of the places that are NOT NaNs doug On 05/21/2013 09:37 AM, Glen Lee wrote: Inline image 1 Hi freesurfer experts, I'm dealing with an issue with smoothing on surface data that unfortunately contain 'NaN' in the ventral temporal region (which is a region that we are interested in). This may be due to the slab data acquisition, where the bottom of the slice meant to be at the bottom of the tomporal lobe for every subject. Apparently, we didn't quite succeed in this as we saw missing data points that are filled with 'NaN' during 2D reconstruction in some subjects' 2D data. In the cartoon above, the yellow color depicts vertices with 'NaN' in the ventral temporal region , and you can easily see how this is affected by smoothing (4mm FWHM), such that a large swath of ventral regions have NaNs after smoothing. I've tried smoothing both with and without --cortex flag, but the results were the same regardless. So, the best bet would be masking out those NaN vertices before smoothing and I wonder if there is any way of doing it in freesurfer. Otherwise, I may need to consider smoothing outside of the freesurfer using Matlab (but I have no experience about this approach). If anyone has previously dealt with this issue (hope I'm not the only one) and know how to get around with it either inside or outside of the freesurfer, please help me. -Glen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error in longitudinal processing dimension mismatch
Dear Martin, Thank you for your helpful information. You were right that something had gone wrong with my preprocessing (for some unknown reasons). I re-run the preprocessing and was able to get the long_mris_slopes command up-and-running. Keith On Wed, May 8, 2013 at 4:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Keith, your longitudinal qdec file looks OK. Something must have gone wrong before (in the processing, e.g. maybe the base was reprocessed and the longs were not updated or things were renamed?) I would create a new directory with only this subject, then start from scratch. create both cross (kp5 and kp5b), the base (kp5_base) and both longs with the correct naming . Then check if the long_mris_slopes command still fails. Best, Martin On 05/01/2013 12:11 PM, Qi Wu wrote: Dear Freesurfer experts, I have a dataset of 2 time points. I ran into problems when I tried to use the two-stage approach to pull out statistics such as the rate of change in Freesurfer 5.1. I could not even get the first stage working. The error messages I got were “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit did not work?” I did further trouble-shooting for this particular message nv1 = 140942, nv1 = 143525, and I found out that 143525 was in the base folder (kp5_base), and 140942 was for the two longitudinally registered images (kp5.long.kp5_base, and kp5b.long.kp5_base). The command line I used was : “long_mris_slopes --qdec ./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”. The first three lines in the qdec file: “fsid fsid-base weeks age sex FSS avgPain kp5 kp5_base 0 48 0 4.1 7 kp5b kp5_base 20 48 0 8.6 6” This error was similar to what was in a previous post ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.htmlby joost janssen Jun 29, 2012). I tried to fix any similar problems, but still wasn’t able to get it working. What else could I have been doing wrong? The on screen error output is provided as follows Many thanks Keith Postdoctoral fellow Toronto Western Hospital Toronto, Ontario Canada *** Parsing the qdec table: ./qdec/AS_long_qdec.dat Working in SUBJECTS_DIR: /data/keith/freesurferdata/subjects_longitudinal_5.1_old Subject-Template: kp5_base INFO: 2 TPs in kp5_base , mean age: 10.0 === SUBJECT kp5_base Intersecting Within-Subject Cortex Label cp /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label mris_label_calc intersect /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label LabelWrite: saving to /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label === SUBJECT kp5_base Stackinbg Within-Subject Maps mri_concat /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness --o /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh === SUBJECT kp5_base Running Within-Subject GLM Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ... mri_glmfit --y /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof --no-contrasts-ok --surf kp5_base lh --label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm Reading source surface /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.white Number of vertices 143525 Number of faces 287046 Total area 91438.851562 AvgVtxArea 0.637094 AvgVtxDist 0.873064 StdVtxDist 0.245806 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old cmdline mri_glmfit --y /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh --X
Re: [Freesurfer] tensor fitting with dt_recon: skull strip
Hi Vincent, I don't think it is supposed to be. Is that a problem? doug On 05/21/2013 09:02 AM, Vincent Koppelmans wrote: Dear FreeSurfer experts, I have used dt_recon for tensor fitting of my diffusion data. I used the following syntax: dt_recon --i dwi.nii.gz --b data.bval data.bvec --s subject_ID --o /DTI --no-reg --no-tal When I inspect the FA data, the tensor fitting itself looks good, but the data is not skull stripped: FA map: mask: I was wondering if I did something wrong and how I should fix this. Thanks for your help. Best, Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
Hi!
I am trying to work around this now using more control points.
However, I was wondering whether the fixed version of mri_segment for
v4.5 that accepts the -p parameter is still available? Just in case I
need to use a different threshold at some point.
Thanks, Caspar
2013/5/17 Caspar M. Schwiedrzik cschwie...@rockefeller.edu:
Hi Bruce,
I only put them in because it was not working without them and that
was the solution in the previous discussion.
To summarize: Once I put in -p 0.7, mri_segment misinterprets 0.7 as
the input file name, no matter whether I use -i or not.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Try leaving out the -i and -seg
Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that not for version 4.5?
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
mri_segment: could not read source volume from .700
../mri/brain.mgz: Permission denied
if I add a -i to the input volume, it says flag not recognized.
to get a floating point number into my tcsh script, I am using `echo
7/10 | bc -l`
according to this previous discussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what happens? Can you send the full screen output?
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to
add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
what is your command line? You are probably better off setting
gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
html),
but now it does not recognize the -i flag.
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Hard to fix if that is the receive field and you don't have
another
image
like a T2w to remove it with. Perhaps mri_normalize can be tuned
to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I
have
almost no experience analyzing monkey brains at .5mm, so I'm
really
not
sure what to advise you. Perhaps one of the other people on list
who
have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I tried adding control points in the white matter in that
region,
however, it does not seem to fix the issue. Also, the
brainmask.mgz
does not seem to exclude this part of the brain, so that is not
the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate
the
problem.
White matter pixel values range from the high 80ies to 100 in
this
area.
Included grey matter pixel values are in the low 80ies.
Excluded grey matter pixel values range from the low 60ies to
low
70ies.
Would it make sense to re-run mri_segment
[Freesurfer] Overlay thickness for BA areas
Hello list! Is there a way to display the thickness of individual Bordmann areas in the inflated surface using tksurfer? I'm able to show surface area with File- Label - Load label and choosing the thresholded label. Now, I qould like to do the same but with cortical thickness, is this possible? I'm using FS 5.0. Thank you in advance, Andreia ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Overlay thickness for BA areas
Hi Andreia, do you mean that you want to display a constant value in each BA on the surface? We don't haveanything explicit to do that, but you could do it in matlab. Let me know if you need more info. doug On 05/21/2013 11:46 AM, _andre...@sapo.pt wrote: Hello list! Is there a way to display the thickness of individual Bordmann areas in the inflated surface using tksurfer? I'm able to show surface area with File- Label - Load label and choosing the thresholded label. Now, I qould like to do the same but with cortical thickness, is this possible? I'm using FS 5.0. Thank you in advance, Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] usage of mri_segstats
Hello list! Can I use the command mri_segstats to calculate the statistics across multiple subjects? If yes, how to do it? Thank you in advance, Fang ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Overlay thickness for BA areas
Hi Doug, I would like to have the thickness map restricted to the BAs where the group differences showed up. Could it be possible to overlay the thickness map of an individual and then restrict it to the chosen BA, for example? The ideia is to have two subjects with the thickness overlayed for display purposes. If there would be a way to do this by groups it would also be nice! Thank you! Andreia Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Hi Andreia, do you mean that you want to display a constant value in each BA on the surface? We don't haveanything explicit to do that, but you could do it in matlab. Let me know if you need more info. doug On 05/21/2013 11:46 AM, _andre...@sapo.pt wrote: Hello list! Is there a way to display the thickness of individual Bordmann areas in the inflated surface using tksurfer? I'm able to show surface area with File- Label - Load label and choosing the thresholded label. Now, I qould like to do the same but with cortical thickness, is this possible? I'm using FS 5.0. Thank you in advance, Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all errors: v5.0.0
1) BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 === 2)*WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 == 3)CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] usage of mri_segstats
Hi Fang, mri_segstats can only be run on individual subjects, but you could easily write a script to run it on all your subjects, then use asegstats2table to merge all the individual subject stats into a spreadsheet ready table. -Louis On Tue, 21 May 2013, Fang CAO wrote: Hello list! Can I use the command mri_segstats to calculate the statistics across multiple subjects? If yes, how to do it? Thank you in advance, Fang ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit application in the two-stage longitudinal approach
Hi Martin, Now I move onto the mri_glmfit step (still within the two stage method). The on-line tutorial for doing this is not very clear. The output of the first stage is stored in the subject-template (base), already in fsaverage space. Simply replace the thickness file with your long.thickness-pc1fit (etc) and run your analysis. For the normal group analysis, one mgh file (the stacked image for all subject for each hemisphere) is created under the SUBJECT folder after the mri_prepro, and the mri_surf2surf steps. However, I assume that after the long_mris_slopes command, the mgh file (lh.long.thickness-spc.fwhm5.fsaverage.mgh, etc.) saved within each subject's base/surf folder is just for that subject. Right? My question is: what is the right way to process these subject specific mgh files within mri_glmfit? How to design the FSGD file for this particular glmfit? I appreciate your clarification on this issue, and I do believe that it would be very helpful if you could add your clarification onto the online tutorial for the two stage method ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) Many thanks Keith On Wed, May 8, 2013 at 4:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Keith, your longitudinal qdec file looks OK. Something must have gone wrong before (in the processing, e.g. maybe the base was reprocessed and the longs were not updated or things were renamed?) I would create a new directory with only this subject, then start from scratch. create both cross (kp5 and kp5b), the base (kp5_base) and both longs with the correct naming . Then check if the long_mris_slopes command still fails. Best, Martin On 05/01/2013 12:11 PM, Qi Wu wrote: Dear Freesurfer experts, I have a dataset of 2 time points. I ran into problems when I tried to use the two-stage approach to pull out statistics such as the rate of change in Freesurfer 5.1. I could not even get the first stage working. The error messages I got were “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit did not work?” I did further trouble-shooting for this particular message nv1 = 140942, nv1 = 143525, and I found out that 143525 was in the base folder (kp5_base), and 140942 was for the two longitudinally registered images (kp5.long.kp5_base, and kp5b.long.kp5_base). The command line I used was : “long_mris_slopes --qdec ./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”. The first three lines in the qdec file: “fsid fsid-base weeks age sex FSS avgPain kp5 kp5_base 0 48 0 4.1 7 kp5b kp5_base 20 48 0 8.6 6” This error was similar to what was in a previous post ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.htmlby joost janssen Jun 29, 2012). I tried to fix any similar problems, but still wasn’t able to get it working. What else could I have been doing wrong? The on screen error output is provided as follows Many thanks Keith Postdoctoral fellow Toronto Western Hospital Toronto, Ontario Canada *** Parsing the qdec table: ./qdec/AS_long_qdec.dat Working in SUBJECTS_DIR: /data/keith/freesurferdata/subjects_longitudinal_5.1_old Subject-Template: kp5_base INFO: 2 TPs in kp5_base , mean age: 10.0 === SUBJECT kp5_base Intersecting Within-Subject Cortex Label cp /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label mris_label_calc intersect /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label LabelWrite: saving to /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label === SUBJECT kp5_base Stackinbg Within-Subject Maps mri_concat /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness --o /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh === SUBJECT kp5_base Running Within-Subject GLM Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ...
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
Perhaps the problem has already been solved but I just ran into the same issue (on OS X 10.8.2). After poking around, what I found was that while the current AFNI distribution does not have a file named 3dvolreg.afni, it does have one named 3dvolreg. I'm guessing the problem is that it has been renamed. I fixed the problem by creating a link: ln 3dvolreg 3dvolreg.afni I suppose FSFAST needs to be updated to take this new name into account. Cheers! Joe Hi Doug, Here's the output from cat /proc/version: Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012 This is the result of cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Thanks. -Yuhong On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: which version of CentOS? Also, can you send me the result of cat $FREESURFER_HOME/build-stamp.**txt On 03/21/2013 02:09 PM, Y.V. Jiang wrote: Hi Doug, I am using Linux: x86_64 GNU/Linux. Thanks. -Yuhong On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: what platform are you using? On 03/21/2013 01:24 PM, Y.V. Jiang wrote: Hi Doug, Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr -Yuhong On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: Hi Doug, I was running preproc-sess in the newly released freesurfer-5.2.0. The command I used was: preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr -mni305 -fwhm 6 -per-run The program failed with the following errors: 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix 004/tmp.mc-afni2.29239/outvol.**nii.gz 004/tmp.mc-afni2.29239/invol.**nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command. I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is another file of the same name under afni/bin. Preproc-sess is relying on the version in $FREESURFER_HOME/bin. Do you know what the problem is? Should I replace freesurfer's copy of 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? Thanks. -Yuhong __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Re: [Freesurfer] mri_glmfit application in the two-stage longitudinal approach
Hi Keith, you are right, the lh.long.thickness-spc.fwhm5.fsaverage.mgh in each base folder is only for that subject. You process this the same way as you'd usually do thickness in a cross sectional analysis. Except you can skip the mris_prepoc step (as everyting is mapped to fsaverage and presmoothed already, when using the qcache flag to long_mris_slopes). You have several options - simply use mri_concat to stack those files to create the stack - or (probably easier) tell long_mris_slopes to do the job for you with the --stack-rate or --stack-spc etc. options Then you have a stack on fsaverage with the right smoothing level(s). the FSGD file is also as usual, make sure the order of your subjects agrees with the order in the long.qdec table used for the stacking. Added that to the wiki , thanks. Best, Martin On 05/21/2013 02:36 PM, Qi Wu wrote: Hi Martin, Now I move onto the mri_glmfit step (still within the two stage method). The on-line tutorial for doing this is not very clear. The output of the first stage is stored in the subject-template (base), already in fsaverage space. Simply replace the thickness file with your long.thickness-pc1fit (etc) and run your analysis. For the normal group analysis, one mgh file (the stacked image for all subject for each hemisphere) is created under the SUBJECT folder after the mri_prepro, and the mri_surf2surf steps. However, I assume that after the long_mris_slopes command, the mgh file (lh.long.thickness-spc.fwhm5.fsaverage.mgh, etc.) saved within each subject's base/surf folder is just for that subject. Right? My question is: what is the right way to process these subject specific mgh files within mri_glmfit? How to design the FSGD file for this particular glmfit? I appreciate your clarification on this issue, and I do believe that it would be very helpful if you could add your clarification onto the online tutorial for the two stage method (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) Many thanks Keith On Wed, May 8, 2013 at 4:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote: Hi Keith, your longitudinal qdec file looks OK. Something must have gone wrong before (in the processing, e.g. maybe the base was reprocessed and the longs were not updated or things were renamed?) I would create a new directory with only this subject, then start from scratch. create both cross (kp5 and kp5b), the base (kp5_base) and both longs with the correct naming . Then check if the long_mris_slopes command still fails. Best, Martin On 05/01/2013 12:11 PM, Qi Wu wrote: Dear Freesurfer experts, I have a dataset of 2 time points. I ran into problems when I tried to use the two-stage approach to pull out statistics such as the rate of change in Freesurfer 5.1. I could not even get the first stage working. The error messages I got were “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit did not work?” I did further trouble-shooting for this particular message nv1 = 140942, nv1 = 143525, and I found out that 143525 was in the base folder (kp5_base), and 140942 was for the two longitudinally registered images (kp5.long.kp5_base, and kp5b.long.kp5_base). The command line I used was : “long_mris_slopes --qdec ./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”. The first three lines in the qdec file: “fsid fsid-base weeks age sex FSS avgPain kp5 kp5_base 0 48 0 4.1 7 kp5b kp5_base 20 48 0 8.6 6” This error was similar to what was in a previous post (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.html by joost janssen Jun 29, 2012). I tried to fix any similar problems, but still wasn’t able to get it working. What else could I have been doing wrong? The on screen error output is provided as follows Many thanks Keith Postdoctoral fellow Toronto Western Hospital Toronto, Ontario Canada *** Parsing the qdec table: ./qdec/AS_long_qdec.dat Working in SUBJECTS_DIR: /data/keith/freesurferdata/subjects_longitudinal_5.1_old Subject-Template: kp5_base INFO: 2 TPs in kp5_base , mean age: 10.0 === SUBJECT kp5_base Intersecting Within-Subject Cortex Label cp /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label mris_label_calc intersect /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label
[Freesurfer] FreeSurfer v5.3.0
Hello I am interested in downloading the FreeSurfer v5.3.0. I will be running it on a virtual machine platform in Windows (xubuntu). Are there any specific instructions for this on the FreeSurfer website because I noticed it runs on CentOS 6 x86_64 (64b). Or does the download come with the virtual machine? Thank you for your help, Kristina ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FreeSurfer v5.3.0
Kristina, We havent created a Windows Virtual Machine freesurfer bundle yet, but if you already have, or know how to create, an xubuntu vm instance on windows, then all you have to do is download and install the centos distribution from within that xubunbtu instance. if your xubuntu is 32, then you'll want to the centos 4 distribution, not the one with x86_64 in the name. Nick On Tue, 2013-05-21 at 12:28 -0700, Kristina Nalbandian wrote: Hello I am interested in downloading the FreeSurfer v5.3.0. I will be running it on a virtual machine platform in Windows (xubuntu). Are there any specific instructions for this on the FreeSurfer website because I noticed it runs on CentOS 6 x86_64 (64b). Or does the download come with the virtual machine? Thank you for your help, Kristina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Overlay thickness for BA areas
You can create a binary mask from the labels (see mri_label2label with the --outmask option), then run mri_glmfit with the --mask option to only analyze data inside the mask. doug On 05/21/2013 12:19 PM, _andre...@sapo.pt wrote: Hi Doug, I would like to have the thickness map restricted to the BAs where the group differences showed up. Could it be possible to overlay the thickness map of an individual and then restrict it to the chosen BA, for example? The ideia is to have two subjects with the thickness overlayed for display purposes. If there would be a way to do this by groups it would also be nice! Thank you! Andreia Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Hi Andreia, do you mean that you want to display a constant value in each BA on the surface? We don't haveanything explicit to do that, but you could do it in matlab. Let me know if you need more info. doug On 05/21/2013 11:46 AM, _andre...@sapo.pt wrote: Hello list! Is there a way to display the thickness of individual Bordmann areas in the inflated surface using tksurfer? I'm able to show surface area with File- Label - Load label and choosing the thresholded label. Now, I qould like to do the same but with cortical thickness, is this possible? I'm using FS 5.0. Thank you in advance, Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] question abt dt-recon
Hello All, I havent used dt-recon yet but I have a question abt it. When the dt-recon computes the FA maps, whats the dimensions of these FA maps ? Are they resampled to the freesurfer anatomical voxel size (1x1x1) or are they in their native voxel size (in which they were collected) ? If I want to extract say the meanFA from one of the ROIs that freesurfer dumps in aseg/wmparc, can I do that ? Thanks Ri ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] question abt dt-recon
The native DTI space. doug On 05/21/2013 04:41 PM, Ritobrato Datta wrote: Hello All, I havent used dt-recon yet but I have a question abt it. When the dt-recon computes the FA maps, whats the dimensions of these FA maps ? Are they resampled to the freesurfer anatomical voxel size (1x1x1) or are they in their native voxel size (in which they were collected) ? If I want to extract say the meanFA from one of the ROIs that freesurfer dumps in aseg/wmparc, can I do that ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
It should be in $FREESURFER_HOME/bin/3dvolreg.afni On 05/21/2013 02:49 PM, Joseph Dien wrote: Perhaps the problem has already been solved but I just ran into the same issue (on OS X 10.8.2). After poking around, what I found was that while the current AFNI distribution does not have a file named 3dvolreg.afni, it does have one named 3dvolreg. I'm guessing the problem is that it has been renamed. I fixed the problem by creating a link: ln 3dvolreg 3dvolreg.afni I suppose FSFAST needs to be updated to take this new name into account. Cheers! Joe Hi Doug, Here's the output from cat /proc/version: Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012 This is the result of cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Thanks. -Yuhong On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.eduwrote: which version of CentOS? Also, can you send me the result of cat $FREESURFER_HOME/build-stamp.**txt On 03/21/2013 02:09 PM, Y.V. Jiang wrote: Hi Doug, I am using Linux: x86_64 GNU/Linux. Thanks. -Yuhong On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu wrote: what platform are you using? On 03/21/2013 01:24 PM, Y.V. Jiang wrote: Hi Doug, Thanks for the reply. From the command line the command 3dvolreg.afni returned the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr -Yuhong On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu wrote: Hi Yuhong, What happens when you run 3dvolreg.afni from the command line without any args? doug On 03/21/2013 12:38 PM, Y.V. Jiang wrote: Hi Doug, I was running preproc-sess in the newly released freesurfer-5.2.0. The command I used was: preproc-sess -sf sessid -df sessdir -fsd bold -surface fsaverage lhr -mni305 -fwhm 6 -per-run The program failed with the following errors: 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix 004/tmp.mc-afni2.29239/outvol.**nii.gz 004/tmp.mc-afni2.29239/invol.**nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command. I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. There is another file of the same name under afni/bin. Preproc-sess is relying on the version in $FREESURFER_HOME/bin. Do you know what the problem is? Should I replace freesurfer's copy of 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? Thanks. -Yuhong __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu
Re: [Freesurfer] tracula error
Hi Skyler - When you say it's been working fine, have you checked that the orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz, like in the snapshot that I sent you? If those orientations aren't correct, the gradient table isn't correct either. a.y On Tue, 21 May 2013, Skyler Gabriel Shollenbarger wrote: Hi Anastasia, Thank you for all of your help! 'trac-all' has been working fine with the other subjects, so it doesn't appear to be the gradient vector file. Yes, unfortunately the resolution is not the best. Would you consider this subject a loss or are there other fixes you suggest? Thanks again! Skyler - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: sholl...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 21, 2013 10:40:59 AM Subject: Re: [Freesurfer] tracula error Hi Skyler - A couple of things. I'm attaching a screenshot of the FA map and primary tensor eigenvectors of your subject. First, it looks like your gradient directions are incorrect, given how the eigenvectors are oriented in the corpus callosum (yellow arrows in the coronal and axial slice). The eigenvectors follow the shape of the corpus callosum in the axial view but not in the coronal view. My guess is your gradient vectors need to be flipped in the z-direction. Second, your resolution is 4mm. There's going to be a lot of partial voluming. You'll have to give up on the thinner tracts, like ccg/cab (see purple arrow in sagittal view pointing to cingulum, you can barely resolve it from the corpus callosum). Third, you have 14 gradient directions, so fitting the ball-and-stick model to this data, which is done by bedpostx and which you need for the tract reconstruction step, is going to be challening. I don't want to discourage you, but tractography may be a bit more than this data can support. Please let me know if you have more questions, a.y On Mon, 20 May 2013, sholl...@uwm.edu wrote: Hi Anastasia, They were uploaded. Thanks for your help! Skyler Sent from my iPhone On May 20, 2013, at 10:20 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Skyler - If you upload the dmri/dmri.bedpostX/dlabel/scripts directories of your subject for me, I'll take a look. http://gate.nmr.mgh.harvard.edu/filedrop2/ a.y On Fri, 17 May 2013, sholl...@uwm.edu wrote: Hi Anastasia, The brain mask looks fine. Any other suggestions? Thanks for your help, Skyler Sent from my iPhone On May 17, 2013, at 12:24 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Skyler - How does the brain mask look like? Any major chunks of brain missing in the area of the left uncinate? That's the tract where the error occurs, and based on this info in the log file, I'm guessing it's a masking issue: [...] INFO: Rejected 4221 streamlines for straying off mask INFO: Rejected 2 streamlines for reversing direction INFO: Rejected 9 streamlines as length outliers INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) [...] Hope this helps, a.y On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote: Hi all, We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. Thank you in advance! Skyler The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer v5.3.0
Kristina, I do not know what virtual machine manager you intend to use. If you will use Oracle's VirtualBox I would like to share my recent experience with you. I tried a updated CentOS6 virtual machine with Freesurfer 5.2 running under Fedora 18 as host but I had problems during recon-all tests. I also downloaded an old Xubuntu virtual machine file with Freesurfer 5.1 from Freesurfer ftp site and no luck again. I decided to buy a second hard disk and installed CentOS6 in this disk making a dual boot system (Fedora 18 and CentOS6). Freesurfer runs over CentOS6 with no problem in my machine. So I guess the problem was with VirtualBox. With Freesurfer 5.3 release it runs over Fedora 18 too. So if you find problems with your virtual machine best chances are the VM manager is the culprit. If possible I guess running Freesurfer over CentOS6 in a real machine would be better. Marcos Em Ter, 2013-05-21 às 12:28 -0700, Kristina Nalbandian escreveu: Hello I am interested in downloading the FreeSurfer v5.3.0. I will be running it on a virtual machine platform in Windows (xubuntu). Are there any specific instructions for this on the FreeSurfer website because I noticed it runs on CentOS 6 x86_64 (64b). Or does the download come with the virtual machine? Thank you for your help, Kristina ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
