Re: [Freesurfer] Fwd: DICOM unpacking error
Luc, it is missing the pixel spacing (ie, voxel size), which is a
fundamental quantity which should not be missing. Have you anonymized
the data or done something else too it?
doug
On 6/17/13 2:36 PM, Luc Amdahl wrote:
-- Forwarded message --
From: *Luc Amdahl* luc.amd...@gmail.com mailto:luc.amd...@gmail.com
Date: Mon, Jun 17, 2013 at 3:45 PM
Subject: Re: [Freesurfer] DICOM unpacking error
To: Bruce Fischl fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
Hi Bruce,
Thanks for responding.
Here is the command line and screen output:
[Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdcmdir -src
DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii
-run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run
10 bold nii f.nii
$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
/Users/lab/MRI/Solar_System
-src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii
f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii
f.nii -run 10 bold nii f.nii
Fri Jun 14 09:47:20 EDT 2013
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2013/06/14-13:47:20-GMT BuildTimeStamp:
May 13 2013 16:45:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05
21:55:16 mreuter Exp $ User: lab Machine:
Sheinberg-Lab-MRI-iMac.local Platform: Darwin PlatformVersion:
10.8.0 CompilerName: GCC CompilerVersion: 4
Sheinberg-Lab-MRI-iMac.local
Darwin Sheinberg-Lab-MRI-iMac.local 10.8.0 Darwin Kernel Version
10.8.0: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
Fri Jun 14 09:47:20 EDT 2013
Log File is subj_4/unpack.log
INFO: Logfile is subj_4/unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is subj_4/dicomdir.sumfile
INFO: status file is subj_4/parse.status
Scanning directory Fri Jun 14 09:47:20 EDT 2013
mri_parse_sdcmdir --sortbyrun --d DICOM --o subj_4/dicomdir.sumfile
--status subj_4/parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34
36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68
70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Fri Jun 14 09:48:46 EDT 2013
--
1localizer ok 512 512 3 1 59198979
2 T1_MEMPRAGE_freesurfer ok 256 256 176 4
tel:256%20256%20176%20%C2%A0%204 59199008
3 T1_MEMPRAGE_freesurfer ok 256 256 176 4
tel:256%20256%20176%20%C2%A0%204 59187534
4 T1_MEMPRAGE_freesurfer ok 256 256 176 1
tel:256%20256%20176%20%C2%A0%201 59175542
5ep_TR2500_128 ok 64 64 42 128 59175096
6ep_TR2500_128 ok 64 64 42 128 59170659
7ep_TR2500_128 ok 64 64 42 128 59169456
8ep_TR2500_128 ok 64 64 42 128 59168253
9ep_TR2500_128 ok 64 64 42 128 59167050
10ep_TR2500_128 ok 64 64 42 128 59162613
11ep_TR2500_113 ok 64 64 42 113 59299072
12 t2_3DFLAIR ok 256 240 176 1
tel:256%20240%20176%20%C2%A0%201 59297629
unpacking config --
{5 bold nii f.nii} {6 bold nii f.nii} {7 bold nii f.nii} {8 bold nii
f.nii} {9 bold nii f.nii} {10 bold nii f.nii}
---
-
Run 5 -
Fri Jun 14 09:48:46 EDT 2013
5 bold nii f.nii
ERROR: reading DICOM/59175096 tag 28 30
Here is the version of FS I'm using:
freesurfer-i386-apple-darwin10.8.0-stable5-20130513
What exactly do you mean when you ask where the DICOM's are from? I
receive them from Brown's MRF facility, and we've been successful in
converting them on other iMac's using the same version of FS.
Thanks,
Luc
On Mon, Jun 17, 2013 at 2:36 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:
can you send the complete command line and screen output, and tell
us what version of FS you are using and where the dicoms are from?
On Mon, 17 Jun 2013, Luc Amdahl wrote:
Hi Freesurfers,
I am trying to use Freesurfer to convert DICOM files to nii
f.nii files.
Freesurfer is able to find all the DICOM files but always
gives me an error:
ERROR: reading DICOM/59175096 tag 28 30.
Can anyone help?
Thanks,
Luc
--
Luc Amdahl
Brown University '14
Sc.B. Neuroscience
69 Brown St., #6137
Providence, RI 02912
603.252.4441 tel:603.252.4441
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Re: [Freesurfer] 回复: SPM ROI to Cortical Thickness
Hi Bo, you should run the MNI152 template through recon-all, then map your mask to the surface, create a label, then map the label to each individual subject with mri_label2label doug On 6/17/13 7:24 PM, xiangbo_2...@126.com wrote: I analysis the volume of grey matter, and MNI152 as the mask of whole brain. Thanks! Bo 发送自我的HTC One SU - Reply message - 发件人： Bruce Fischl fis...@nmr.mgh.harvard.edu 收件人： xiangbo_2010 xiangbo_2...@126.com 抄送： freesurfer freesurfer@nmr.mgh.harvard.edu 主题： [Freesurfer] SPM ROI to Cortical Thickness 日期： 周二, 6 月 18 日, 2013 年 09:51 And what is the data you analyzed in spm? You could use the mni space mask but it won't be very accurate. On Jun 17, 2013, at 8:44 PM, xiangbo_2010 xiangbo_2...@126.com mailto:xiangbo_2...@126.com wrote: Hi Bruce I use the SPM to analysis my data, and use the xjview to get a mask (have .img and .hdr files) as ROI, use the MNI space in SPM analysis. Following I want to obtain the cortical thickness from this mask in Freesurfer, and I have analyzed all my individual subjects in FreeSurfer(recon-all). thanks! Bo At 2013-06-18 02:35:40,Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: can you give a complete description of your study and what you are trying to achieve? Have you analyzed all your individual subjects in FreeSurfer (recon-all)? What is the mask you want to use? On Tue, 18 Jun 2013, xiangbo_2010 wrote: I want to obtain the cortical thickness from a group of subjects, thanks! At 2013-06-18 00:13:08,Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: are you trying to do this for a single subject or for a group of subjects , or group average data? On Tue, 18 Jun 2013, xiangbo_2010 wrote: my subject has finished the recon-all on the structural image, whether us e the command: mri_vol2surf --src sig.img --src_type analyze --srcreg register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int ro und --trgsubject ico --icoorder 7 to obtain the result? thanks! Bo At 2013-06-18 00:00:09,Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: and what subject do you wan to obtain thickness measures from? You could use mri_vol2vol to map your mask to the individual using the MNI transform On Mon, 17 Jun 2013, xiangbo_2010 wrote: the mask was obtained from xjview, and use the MNI space in my study, thanks! Bo At 2013-06-17 23:52:33,Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wro te: sorry, the formatting of your emails is lost in my reader and you may have said this before, but what is the mask of? What space is it in? On Mon, 17 Jun 2013, xiangbo_2010 wrote: I want to get cortical thickness, and have finished the recon-all, and obtained the mask from SPM which include the file with .img and .hd r, whether I should convert the file (.img and .hdr) to file (.nii), a nd use the command: bbregister --s bert --mov func.nii --init-spm --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf to obtain the result? thanks! Bo At 2013-06-17 23:07:19,Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wro te: please cc the list so others can answer. Do you mean get cortical thickness? If so, then you need to run recon-all on the structural im age On Mon, 17 Jun 2013, xiangbo_2010 wrote: I have obtained the mask from xjview (.img), I want to obtain th e C T f rom the mask, thanks! Bo At 2013-06-17 22:40:43,Bruce Fischl fis...@nmr.mgh.harvard.ed mailto:fis...@nmr.mgh.harvard.ed u wro te: what are you trying to map to the surface? On Mon, 17 Jun 2013, xiangbo_2010 wrote: Hi Bruce Thank you for my help, when I use the bbregister, do not know ho w t o c hoo se data for --mov, thanks! Bo At 2013-06-17 20:34:39,Bruce Fischl fis...@nmr.mgh.harvard mailto:fis...@nmr.mgh.harvard .ed u wro te: Hi Bo, tksurfer doesn't take a path to a file. Read the help on it - y ou nee d t o reconstrcut the subject with recon-all then give it the subj ect id . To project a volumetric map onto the surface use mri_vol2surf, wit h t he registration typically computed by bbregister. cheers Bruce On Mon, 17 Jun 2013, xiangbo_2010 wrote: Hi dougThank you for giving this information, I used the command: /tksurfer fsaverage lh inflated -aparc -mni152reg -ov erl ay /pa thn ame/to/s pm/roi/yourfile.img/, but do not have results for me, and do no t k now
Re: [Freesurfer] nifti1Read(): unsupported slice timing pattern 5
Hi Mariam, I don't know why it does not read this particular code. I can modify it when I get back from HBM and send you a new version of mri_convert. Or you might be able to change the way you convert from BRIK to use a different slice code. doug On 6/17/13 4:13 PM, Mariam Sood wrote: Hello everyone, I was trying out FS-FAST tutorial with my set of images (converted to NIFTI from AFNI BRIK format using 3dAFNItoNIFTI). However, I get this error 'nifti1Read(): unsupported slice timing pattern 5 in … '. Looking at NIFTI.h, this value (#define NIFTI_SLICE_ALT_INC2 5) is added to cater for acquisition schemes in some siemens scanners (ours is siemens). Why doesn't Freesurfer like this? I looked through the Freesurfer mailing list, but didn't quite find a solution yet. I am new to whole fMRI analysis, so apologies if I am missing something obvious. Many thanks, Mariam. ___ 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] problem downloading Xhemi files
Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If not, I'll have to recreate the links. let me know doug On 6/17/13 6:52 AM, amirhossein manzouri wrote: Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir ___ 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] Tracula bbr errors
Hi Matt, was I supposed to get back to you on this? I generally leave these types of questions to Nick and Zeke. doug ps. Please post to the list instead of us indivudally. thanks! On 6/16/13 12:46 PM, Matthew Hoptman wrote: Hi Dr. Greve, Any news on the libboost_program_options.so.5 issue? I've encountered it using mris_resample (as part of mri_cvs_register) using Linux Mint 14 Best, Matt ___ 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] libboost_program_options.so.5 issue
Hi all,
Any news on the libboost_program_options.so.5 issue, as relates to
mri_cvs_register? I've encountered it using mris_resample (as part of
mri_cvs_register) using.
When I run:
qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V
${FREESURFER_HOME}/bin/mri_cvs_register --mov ${subject}
where ${subject} was found by looping through all of my subjects
I get the error:
mris_resample: error while loading shared libraries:
libboost_program_options.so.5: cannot open shared object file: No such file or
directory
bugr gives me:
FREESURFER_HOME: /home/hoptman/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0beta
Debian version: 6.0.4
Kernel info: Linux 2.6.32-5-amd64 x86_64
Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine
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[Freesurfer] qdec differences in FS 5.0 vs 5.3
Hi, I'm learning how to use QDEC and was comparing results that it produces under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS method of producing a design matrix, while the 5.3 only has DODS. This suggests that results should be identical (or at least similar) across versions if I select DODS. However, I'm getting very different results based on the version I select: complete lack of differences across groups in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like to understand where the differences are stemming from -- any ideas? Thanks in advance! Maria *** Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital ___ 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] Reviewer not satisfied
.H is mean and .K is Gaussian curvature. It should also write a .max and .min, doesn't it? Those are the principal curvatures that you want. Bruce On Tue, 18 Jun 2013, Jürgen Hänggi wrote: Dear Bruce Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files? Cheers Jürgen On [DATE], Bruce Fischl [ADDRESS] wrote: Hi Jürgen you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution. cheers Bruce p.s. I think you want -w -max and -w -min flags for it On Fri, 14 Jun 2013, Jürgen Hänggi wrote: Dear FS experts In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition. We wrote the following: The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter. Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a couple of millimeters. Is this 1-3 mm or rather 3-5 mm or any other value? Thanks in advance for any suggestion Regards Jürgen Hänggi Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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. Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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
[Freesurfer] Group Analysis
Dear Freesurfer group I am interested to do group analysis on my data. If I want to do inter-individual group analysis, what is the minimum number of subjects I need to have? Also if I want to do intra-individual analysis, what is the best way in FS? I appreciate your time and your help. Thanks a lot, Nooshin ___ 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] medial wall crossing surface
Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] medial wall crossing surface
Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] stuck on step to create surface
Hi Jane that means it is trying to correct the topology of a very large defect. 46K vertices is about 1/3 of a normal human hemisphere. Check the ?h.orig.nofix and see if something big has gone wrong - the skull being attached or the cerebellum or something like that. I don't have much experience with NHP data, so hopefully someone else on the list can chime in. cheers Bruce On Tue, 18 Jun 2013, Jane Qu wrote: Hi freesurfers! I am new to freesurfer and have encountered a problem with surface generation. I am working with a non-human primate anatomical volume. I finished segmenting the white matter and am on this next step. I think, however, that the step where the surface is generated from wm.mgz is crashing (I started the process last night and it has not finished and does not appear to be moving forward). Does anybody know why this might be happening? How long should I expect this step to take? I have attached below some of the messages I'm receiving. Thanks in advance! Jane ___ 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] medial wall crossing surface
Hi Celine is the aseg correctly labeled in these regions? Is the filled.mgz? That's a tough case as it's not clear from looking at it which hemi those voxels belong to (probably some of each) Bruce On Tue, 18 Jun 2013, cel...@nmr.mgh.harvard.edu wrote: Sorry here is a snapshot for an example. Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] ERROR! FOV=348.000 256
Hi all, I am coming across this error for couple of my subjects: WARNING ===== The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 348 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/sray2/Data/50183/50183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (0.468746, 0.468746, 1.4) mm size and (512, 512, 248) voxels. Data is conformed to 1 mm size and 348 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/sray2/Data/50183/50183/mri/orig.mgz... ERROR! FOV=348.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Linux localhost.localdomain 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 50183 exited with ERRORS at Sat Jun 15 06:02:30 CDT 2013 Do anyone know whats wrong and how can I fix this? Thanks in advance. -Siddharth ___ 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! FOV=348.000 256
Hello Siddharth, The error message says Include the flag -cw256 with recon-all! So I would recommend giving that a try. -Zeke On 06/18/2013 12:33 PM, Ray, Siddharth wrote: Hi all, I am coming across this error for couple of my subjects: WARNING ===== The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 348 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/sray2/Data/50183/50183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (0.468746, 0.468746, 1.4) mm size and (512, 512, 248) voxels. Data is conformed to 1 mm size and 348 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/sray2/Data/50183/50183/mri/orig.mgz... ERROR! FOV=348.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Linux localhost.localdomain 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 50183 exited with ERRORS at Sat Jun 15 06:02:30 CDT 2013 Do anyone know whats wrong and how can I fix this? Thanks in advance. -Siddharth ___ 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] Temporal Lobe Problem
Hi Lior it looks like you have significant darkening in the MTL complicated by pretty noisy scans. Can you tell us more about what you are doing? What sequences and scanner are you using? What is your subject population? Control points would probably be your best bet, but this might be able to be improved on the acquisition side as well (although it sounds like it's too late for that) cheers Bruce On Tue, 18 Jun 2013, LIOR ZWANZIGER wrote: Hi, I have scans of around 60 participants and about 75% percent of these have significant portions of their temporal lobe excluded. I have attached different slices from four different subjects to give you an idea of the typical scan I've been encountering, [though there are problems in minimally 10 slices for each participant and some exclusions can be found in more than 50 slices.] We are using FreeSurfer version 5.1.0. What is your advice, since there are so many slices for a large number of participants that would need to be edited? Extension of the watershed parameters, adding control points, or something else I haven't considered? I am hesitant to add control points for such a great number of participants. Thank you! Lior Zwanziger ___ 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! FOV=348.000 256
wow, why is your FOV so big? On Tue, 18 Jun 2013, Ray, Siddharth wrote: Hi all, I am coming across this error for couple of my subjects: WARNING ===== The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 348 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/sray2/Data/50183/50183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (0.468746, 0.468746, 1.4) mm size and (512, 512, 248) voxels. Data is conformed to 1 mm size and 348 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/sray2/Data/50183/50183/mri/orig.mgz... ERROR! FOV=348.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Linux localhost.localdomain 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 50183 exited with ERRORS at Sat Jun 15 06:02:30 CDT 2013 Do anyone know whats wrong and how can I fix this? Thanks in advance. -Siddharth ___ 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] sub-parcellation
I just attended the pre-OHBM FSL/FS course, and spoke to David Salat there about possibilities to create more detailed sub-parcellationsfrom the two major structural atlases. Could someone please let me know if David was right that such tools exist, and/or point me to them? My goal is essentially to create relatively equal-area parcellations with say 100, 200, 500, 1000, 2000, 5000, etc. ROIs per hemisphere, retaining some type of labeling to indicate where each ROI came from. Thanks, -Jeff PS I am at the HBM meeting through mid-day Thursday if someone here is able to talk to me in person (maybe even David!). My cell is 971-533-3942 if someone in Seattle wants to call or text. ___ 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] sub-parcellation
Hi Jeff there are two utilities we provide for this (and yes, David is always correct!): 1. mris_make_face_parcellation - create approximately unifom-sized parcels using icosahedral subdivisions. These can be uniform in the native space using the ?h.sphere, or in register and uniform in the group space using ?h.sphere.reg. 2. mris_divide_parcellation - divides an existing annotation file (e.g. lh.aparc.annot) either with a specific set of divisions specified by the user, or so that no individual parcel is greater than a specified surface area. cheers Bruce On Tue, 18 Jun 2013, Jeff Eriksen wrote: I just attended the pre-OHBM FSL/FS course, and spoke to David Salat there about possibilities to create more detailed sub-parcellationsfrom the two major structural atlases. Could someone please let me know if David was right that such tools exist, and/or point me to them? My goal is essentially to create relatively equal-area parcellations with say 100, 200, 500, 1000, 2000, 5000, etc. ROIs per hemisphere, retaining some type of labeling to indicate where each ROI came from. Thanks, -Jeff PS I am at the HBM meeting through mid-day Thursday if someone here is able to talk to me in person (maybe even David!). My cell is 971-533-3942 if someone in Seattle wants to call or text. ___ 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] medial wall crossing surface
Hi Bruce The aseg is correctly labeled as regards right and left GM cortex, but definitely some voxels are belonging to both hemisphere. The filled.mgz is fine too. Should we delete from aseg the voxels that are at the border between the lh and rh? Thanks Celine Hi Celine is the aseg correctly labeled in these regions? Is the filled.mgz? That's a tough case as it's not clear from looking at it which hemi those voxels belong to (probably some of each) Bruce On Tue, 18 Jun 2013, cel...@nmr.mgh.harvard.edu wrote: Sorry here is a snapshot for an example. Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] medial wall crossing surface
Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemi cheers Bruce On Tue, 18 Jun 2013, cel...@nmr.mgh.harvard.edu wrote: Hi Bruce The aseg is correctly labeled as regards right and left GM cortex, but definitely some voxels are belonging to both hemisphere. The filled.mgz is fine too. Should we delete from aseg the voxels that are at the border between the lh and rh? Thanks Celine Hi Celine is the aseg correctly labeled in these regions? Is the filled.mgz? That's a tough case as it's not clear from looking at it which hemi those voxels belong to (probably some of each) Bruce On Tue, 18 Jun 2013, cel...@nmr.mgh.harvard.edu wrote: Sorry here is a snapshot for an example. Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] ct.anat.nii file
Hi Freesurfers, I'm wondering if there is a way to figure out if a ct.anat.nii file is corrupt or not. I'm using MRICro as a viewer, and the file doesn't look right. Thanks, Mia ___ 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] Mapping annotation files from one subject to another
Hi Louis, When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like mri_annot2annot, does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work. Thanks, Peter On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote: Hi Peter, mri_surf2surf is what you want to use for this. -Louis On Mon, 17 Jun 2013, Peter Savadjiev wrote: Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/file.annot fsaverage /tmp/output.gcs (wherefile andoutput are some file names) and that executed without any problems. Then I ran mris_ca_labelsubject_id lh lh.sphere.reg /tmp/output.gcs ./lh.newfile.annot (heresubject_id is some subjects' name, andoutput andnewfile are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter ___ 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 ___ 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] Mapping annotation files from one subject to another
this is what mri_surf2surf is for. What was your command line? Did you check the help? On Tue, 18 Jun 2013, Peter Savadjiev wrote: Hi Louis, When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like mri_annot2annot, does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work. Thanks, Peter On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote: Hi Peter, mri_surf2surf is what you want to use for this. -Louis On Mon, 17 Jun 2013, Peter Savadjiev wrote: Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/file.annot fsaverage /tmp/output.gcs (wherefile andoutput are some file names) and that executed without any problems. Then I ran mris_ca_labelsubject_id lh lh.sphere.reg /tmp/output.gcs ./lh.newfile.annot (heresubject_id is some subjects' name, andoutput andnewfile are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter ___ 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 ___ 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] Mapping annotation files from one subject to another
Dear Bruce, This is the command line I used: mri_surf2surf --srcsubject fsaverage --srcsurfval Yeo2011_7Networks_N1000.annot --trgsubject case01053 --trgsurfval Yeo2011_7Networks_N1000.annot --hemi lh and I get the error message: ERROR: could not determine type of Yeo2011_7Networks_N1000.annot (I thought I may need to specify the full name, lh.Yeo2011_7Networks_N1000.annot, or even the full pathname, but either way I would get the same error) Any help would be much appreciated, thank you very much! Peter On 06/18/2013 02:51 PM, Bruce Fischl wrote: this is what mri_surf2surf is for. What was your command line? Did you check the help? On Tue, 18 Jun 2013, Peter Savadjiev wrote: Hi Louis, When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like mri_annot2annot, does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work. Thanks, Peter On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote: Hi Peter, mri_surf2surf is what you want to use for this. -Louis On Mon, 17 Jun 2013, Peter Savadjiev wrote: Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/file.annot fsaverage /tmp/output.gcs (wherefile andoutput are some file names) and that executed without any problems. Then I ran mris_ca_labelsubject_id lh lh.sphere.reg /tmp/output.gcs ./lh.newfile.annot (heresubject_id is some subjects' name, andoutput andnewfile are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter ___ 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 ___ 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 ___ 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] Mapping annotation files from one subject to another
Oh, I see what my error was: I need to use --sval-annot instead of --srcsurfval. Thanks! Peter On 06/18/2013 02:51 PM, Bruce Fischl wrote: this is what mri_surf2surf is for. What was your command line? Did you check the help? On Tue, 18 Jun 2013, Peter Savadjiev wrote: Hi Louis, When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like mri_annot2annot, does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work. Thanks, Peter On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote: Hi Peter, mri_surf2surf is what you want to use for this. -Louis On Mon, 17 Jun 2013, Peter Savadjiev wrote: Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/file.annot fsaverage /tmp/output.gcs (wherefile andoutput are some file names) and that executed without any problems. Then I ran mris_ca_labelsubject_id lh lh.sphere.reg /tmp/output.gcs ./lh.newfile.annot (heresubject_id is some subjects' name, andoutput andnewfile are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter ___ 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 ___ 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 ___ 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] Fs Tutorial data bert.recon.tgz md5sum mismatch
Dear freesurfer support group, I keep getting 9a5dcc7ebb7aa8564c4bba47ef0293e9 as the md5sum for the bert.recon.tgz file which I downloaded from the following link ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz The correct md5sum is supposed to be 04d6fa1703787e546aaafbfade17cab2. I downloaded the file several times with different terminals, using the command curl -O. I do get the correct md5sum for fsfast-functional.tar.gz, fbert-feat.tgz, diffusion_recons.tar.gz and diffusion_tutorial.tar.gz. I haven't completed downloading the other three files. I will write to you if I have similar problems, too. Do you, by any chance, have a different version of bert.recon.tgz on that link? Thank you very much! Sincerely, Ye Tian ___ 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] MRIread.m and hippocampal subfields
Hi, Freesurfer experts
If you try to read one of the posterior*.mgz files generated by reco-all
-hippo-subfield into MatLab/Octave using MRIread.m it fails like this:
Ps=MRIread('posterior_left_subiculum.mgz')
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
That is because the posterior*.mgz files does not have this data. I made
a creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
That works but it is only a quick workaround since MRIread,m calls
load_mgh.m and it shows a warning message about the mr_parms. This
message does not block my work but it is not good to see the warning all
the time on my screen. Perhaps the best fix would be just creating the
posterior*.mgz files with these data defined as 0. But I would be happy
if I could just edit these files defining these values. Is there a
freesurfer tool to make this simple edition? I noticed, for example,
that when you use mri_concat to sum these files the resulting
concatenated file is fixed and these parameters are defined.
Thanks in advance,
Marcos.
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Re: [Freesurfer] Fs Tutorial data bert.recon.tgz md5sum mismatch
Dear freesurfer experts, All of my other tutorial files are complete with the correct md5sum except bert.recon.tgz. I re-downloaded bert.recon.tgz, and got the consistent wrong answer again. I highly doubt that something is wrong with my downloading. Would someone please take a look at the original file? Thank you very much! Sincerely, Ye On Tue, Jun 18, 2013 at 4:02 PM, ye tian tianye...@gmail.com wrote: Dear freesurfer support group, I keep getting 9a5dcc7ebb7aa8564c4bba47ef0293e9 as the md5sum for the bert.recon.tgz file which I downloaded from the following link ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz The correct md5sum is supposed to be 04d6fa1703787e546aaafbfade17cab2. I downloaded the file several times with different terminals, using the command curl -O. I do get the correct md5sum for fsfast-functional.tar.gz, fbert-feat.tgz, diffusion_recons.tar.gz and diffusion_tutorial.tar.gz. I haven't completed downloading the other three files. I will write to you if I have similar problems, too. Do you, by any chance, have a different version of bert.recon.tgz on that link? Thank you very much! Sincerely, Ye Tian ___ 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] How to make inflated or white/pial surface of fsaverage atlas
Hi, I have a question about how to make surfaces in shape of inflated or white/pial (fiducial) surface for the fsaverage atlas. In my understanding, to make a population average surface from multiple individual surfaces, the surfaces should be first in shape of sphere. But, I'm not clear how can we obtain population average surface in shape of inflated and original white/pial surface which do not depend on specific individual. This is my question. Freesurfer seems to have such surfaces like inflated.avg or white.avg. And from the logs for creating fsaverage (make_average_surface.log), it seems that this is done by averaging individual surfaces after being transformed into each type of configuration(inflated, white, etc...). But in that case, what was averaged for example in case of averaging inflated surface? 3D coordinate (x,y,z)? But if so, it will lose the topology of cortical surface. If you have any answers or comments to this question, please give some advice. Regards, Tomoyasu HORIKAWA Tomoyasu ATR CNS Dept. of Neuroinformatics ___ 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.
