Re: [Freesurfer] Fwd: LGI path problem
Hi, thank you. I am using Linux. I not sure where to change path, ie which
file this should be done in and where this file is located. This the error
message I recieve, and as I said It is launching the wrong matlab and I
don't know how change this.
Launching Matlab7p13
Warning: Unable to open display 'iconic'. You will not be able to display
graphics on the screen.
M A T L A B (R)
Copyright 1984-2011 The MathWorks, Inc.
R2011b (7.13.0.564) 32-bit (glnx86)
August 13, 2011
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
reading filled volume...
closing volume...
Undefined function 'fspecial' for input arguments of type 'char'.
Error in make_outer_surface (line 31)
Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file
'/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64
x86_64 x86_64 GNU/Linux
recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58 BST 2013
Thank you very much for your time and help,
Kind Regards,Linn
On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer marie.sch...@unige.chwrote:
Hi Linn,
Sorry for the delay in answering. The path has to be set directly in
your environment variable (the variable $PATH has to point to the correct
version). I need a few more details about what you tried and which OS you
are using to be able to help you.
If you are using mac, here is an example on how you can set the path in
the .shrc file:
setenv PATH $PATH:/Applications/MATLAB_R2013b.app/bin
You can also have a look at the following posts:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html
Let me know how it goes,
Marie
On Oct 22, 2013, at 2:41 AM, Linn Mittlestein linnmit...@gmail.com
wrote:
Hi,
I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
exporting the matlab path, however It keeps calling another version of
Matlab. Can someone please tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
-- Forwarded message --
From: Linn Mittlestein linnmit...@gmail.com
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein linnmit...@gmail.comDate: Fri, Oct 18, 2013 at
1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu
Hi,
I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
exporting the matlab path, however It keeps calling another version of
Matlab. Can someone please tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] missing eTIV in asegstats2table
Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel aseg.stats_subj2 Description: Binary data aseg.stats_suj1 Description: Binary data ___ 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 statistics
Dear Anastasia, I tried the command you suggested me and i obtained the output I attach to the mail. I would like to ask you if I understood well shot it means. In this case left uncinatus connects the following cortex areas: ctx-lh-fusiform ctx-lh-inferiortemporal ctx-lh-lateralorbitofrontal ctx-lh-medialorbitofrontal ctx-lh-middletemporal ctx-lh-rostralanteriorcingulate ctx-lh-superiortemporal ctx-lh-temporalpole ctx-lh-insula and for each area I have the volume of the path. Is it correct? Thanks Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 18/ott/2013, alle ore 17:32, Anastasia Yendiki ha scritto: Hi Lucia - You can probably do that with mri_segstats. Try something like: mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz And similarly for any other pathway. See the mri_segstats help for more usage info. Let me know if this gives you what you need. a.y On Fri, 18 Oct 2013, Lucia Billeci wrote: Thanks Anastasia, this is useful for visualization. But to construct a table with for each tracts the parcellation regions that it connects do I need to look at the image? Lucia On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote: Hi Lucia - You can look at the tracula output over the cortical parcellation and subcortical segmentation in the individual's diffusion space like this: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv dpath/merged_avg33_mni_bbr.mgz Hope this helps, a.y On Fri, 18 Oct 2013, Lucia Billeci wrote: Dear Anastasia and all, how can I understand which are the region of the brain in which the brain base been parecellated that each tract generated by TRACULA connect? For example if I look at the left uncinate fascicles how can I know which are the ROIs of the statistical output from the cortical parcellation that it connects? Thanks Lucia On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote: Hi Anastasia, thanks for you answer. Now I have understood the meaning of that parameter. Best regards Lucia On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: Hi Lucia - It's how many sample paths were drawn to produce the probability distribution of the path (path.pd.nii.gz). It depends on the configuration parameters (nsample, nkeep), so it'll be the same if these configuration parameters are the same. Hope this helps, a.y On Mon, 14 Oct 2013, Lucia Billeci wrote: Dear all, I noticed that in the TRACULA statistics output files (pathstats.overall.txt) the variable Count that should indicate the number of sample paths in the WM tract is the same for all the computed tract. Could anyone tell me why this happen? Thanks a lot Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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,
Re: [Freesurfer] TRACULA statistics
Dear Anastasia,I tried the command you suggested me and i obtained the output I attach to the mail.I would like to ask you if I understood well shot it means. In this case left uncinatus connects the following cortex areas:ctx-lh-fusiform ctx-lh-inferiortemporalctx-lh-lateralorbitofrontalctx-lh-medialorbitofrontalctx-lh-middletemporalctx-lh-rostralanteriorcingulatectx-lh-superiortemporalctx-lh-temporalpole ctx-lh-insula and for each area I have the volume of the path. Is it correct?ThanksLucia# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ # cmdline mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --excludeid 0 --sum leftunc.txt --i dpath/lh.unc_AS_avg33_mni_bbr/path.pd.nii.gz # sysname Darwin # hostname Lucia-MAC.area.pi.cnr.it. # machine x86_64 # user luciabilleci # anatomy_type volume # # SegVolFile dlabel/diff/aparc+aseg.bbr.nii.gz # SegVolFileTimeStamp 2013/10/03 10:24:56 # ColorTable /Applications/freesurfer/FreeSurferColorLUT.txt # ColorTableTimeStamp 2013/05/14 16:36:03 # InVolFile dpath/lh.unc_AS_avg33_mni_bbr/path.pd.nii.gz # InVolFileTimeStamp 2013/10/03 14:40:09 # InVolFrame 0 # ExcludeSegId 0 # Only reporting non-empty segmentations # VoxelVolume_mm3 27 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader Mean # TableCol 6 FieldName Intensity Mean # TableCol 6 Units unknown # TableCol 7 ColHeader StdDev # TableCol 7 FieldName Itensity StdDev # TableCol 7 Units unknown # TableCol 8 ColHeader Min # TableCol 8 FieldName Intensity Min # TableCol 8 Units unknown # TableCol 9 ColHeader Max # TableCol 9 FieldName Intensity Max # TableCol 9 Units unknown # TableCol 10 ColHeader Range # TableCol 10 FieldName Intensity Range # TableCol 10 Units unknown # NRows 110 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2 7198 194346.0 Left-Cerebral-White-Matter 4.5893 26.8066 0. 632. 632. 2 4 100 2700.0 Left-Lateral-Ventricle 0.1200 0.6077 0. 4. 4. 3 515 405.0 Left-Inf-Lat-Vent 2.8667 5.5789 0.19.19. 4 7 38010260.0 Left-Cerebellum-White-Matter 0. 0. 0. 0. 0. 5 8 160643362.0 Left-Cerebellum-Cortex 0. 0. 0. 0. 0. 6 10 229 6183.0 Left-Thalamus-Proper 0.1004 0.4986 0. 5. 5. 7 11 117 3159.0 Left-Caudate 1.0855 2.5917 0.21.21. 8 12 206 5562.0 Left-Putamen 5.2913 12.7529 0. 152. 152. 9 1354 1458.0 Left-Pallidum 1.8519 2.1754 0. 8. 8. 10 1431 837.0 3rd-Ventricle 0. 0. 0. 0. 0. 11 1566 1782.0 4th-Ventricle 0. 0. 0. 0. 0. 12 16 55815066.0 Brain-Stem 0. 0. 0. 0. 0. 13 17 116 3132.0 Left-Hippocampus 0.1983 1.1589 0. 9. 9. 14 1867 1809.0 Left-Amygdala 0.8209 2.1315 0.10.10. 15 2418 486.0 CSF0. 0. 0. 0. 0. 16 2627 729.0 Left-Accumbens-area4.2593 6.8027 0.23.23. 17 28 130 3510.0 Left-VentralDC 0. 0. 0. 0. 0. 18 30 3 81.0 Left-vessel9.6667 9.5044 0.19.19. 19 3158 1566.0 Left-choroid-plexus0.0345 0.2626 0. 2. 2. 20 41 7404 199908.0 Right-Cerebral-White-Matter0.0011 0.0930 0. 8. 8. 21 4396 2592.0 Right-Lateral-Ventricle0.0312 0.3062 0. 3. 3. 22 44 6 162.0
Re: [Freesurfer] Extremely intense grey matter being omitted
No, you mean anatomically speaking? If it's unfixable then that's OK, was just wondering if it was possible. On Oct 22, 2013, at 10:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I'm not sure it's fixable then. Any idea what they are? Bruce On Oct 22, 2013, at 9:30 AM, Jonathan Holt whats...@umich.edu wrote: They are bright in orig.mgz. You can see in the pictured attachments On Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)? On Mon, 21 Oct 2013, Jonathan Holt wrote: FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas? I fear it may believe they are dura because of the similar intensity values. jon 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. Screen Shot 2013-10-21 at 2.01.00 PM.png Screen Shot 2013-10-21 at 2.00.45 PM.png ___ 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] Subject processing difference between computers
see http://dx.plos.org/10.1371/journal.pone.0038234 On 22 Oct 2013, at 18:18, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 2 Date: Tue, 22 Oct 2013 16:15:44 + From: West, John D. jdw...@iupui.edu Subject: [Freesurfer] Subject processing difference between computers To: freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: 793d43fe7976404cb5e172709ab1f4081123f...@iu-mssg-mbx102.ads.iu.edu Content-Type: text/plain; charset=us-ascii Hello. We are moving our processing from an older super computer to a new one here at Indiana University. Preliminary testing is showing a significant difference between final summary stats results between subjects processed on the old system versus the new. The version of freesurfer on both systems is identical. Comparing the logs of the same subject run on both systems, I've found that the differences seem to start with the mri_watershed function specifically the main basin size. For the same subject we find: Old computer: main basin size=22667431830 voxels, voxel volume =1.000 = 22667431830 mmm3 = 22667431.936 cm3 New computer: main basin size=22208239350 voxels, voxel volume =1.000 = 22208239350 mmm3 = 22208239.616 cm3 As you can see they are very different. My theory is this is propagating through the rest of the process and giving us different summary stats at the end. I should note that both aseg and aparc stats are affected. I am also enclosing the logs for both runs as well as the differences found through the diff command (this is a lot parse through as even time stamp differences are picked up). Essentially what I am trying to find out is if these differences we are noticing are typical when changing computers and if not what could be causing these differences that I may not be picking up on. Thanks for the help. -John -- next part -- A non-text attachment was scrubbed... Name: recon-all.new.log Type: application/octet-stream Size: 451586 bytes Desc: recon-all.new.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20131022/fe052ee6/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: recon-all.old.log Type: application/octet-stream Size: 450567 bytes Desc: recon-all.old.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20131022/fe052ee6/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: recon-all.diff.log Type: application/octet-stream Size: 319424 bytes Desc: recon-all.diff.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20131022/fe052ee6/attachment-0002.obj ___ 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] reconall error
Hi Rashmi what version are you running? If 5.3, upload the subject and I'll take a look Bruce On Tue, 22 Oct 2013, Rashmi Singh wrote: Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T2Practice/FreeSurfer/AA470-2prac/ mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as 20.2 or 943.7 total sample mean = 92.0 (1443 zeros) spacing=8, using 3481 sample points, tol=1.00e-05... register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 -- 126 resetting gm mean[0]: 74 -- 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) -- (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) -- (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] Extremely intense grey matter being omitted
yes, anatomically. And I would guess it's unfixable without tons of work On Wed, 23 Oct 2013, Jon Holt wrote: No, you mean anatomically speaking? If it's unfixable then that's OK, was just wondering if it was possible. On Oct 22, 2013, at 10:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I'm not sure it's fixable then. Any idea what they are? Bruce On Oct 22, 2013, at 9:30 AM, Jonathan Holt whats...@umich.edu wrote: They are bright in orig.mgz. You can see in the pictured attachments On Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)? On Mon, 21 Oct 2013, Jonathan Holt wrote: FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas? I fear it may believe they are dura because of the similar intensity values. jon 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. Screen Shot 2013-10-21 at 2.01.00 PM.png Screen Shot 2013-10-21 at 2.00.45 PM.png ___ 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] missing eTIV in asegstats2table
Hi Daniel, what is this in reference to? If this is a follow up on a previous thread, please include the rest of the thread and the file in the same email. I go through way too many emails to keep track of who's doing what. thanks! doug On 10/23/13 4:13 AM, Daniel Ferreira wrote: Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel ___ 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] Fwd: LGI path problem
Hi Linn,
If you are using tcsh, you have to edit the file $HOME/.cshrc (.shrc should
work as well) to add the following line:
setenv PATH $PATH:/YOUR_PATH_TO_MATLAB_BIN_DIRECTORY
Then close the terminal and open a new one. Use the env command to be sure that
your path has been modified, then the getmatlab command from FreeSurfer should
give you the correct location.
Best,
Marie
On Oct 23, 2013, at 12:23 AM, Linn Mittlestein
linnmit...@gmail.commailto:linnmit...@gmail.com
wrote:
Hi, thank you. I am using Linux. I not sure where to change path, ie which file
this should be done in and where this file is located. This the error message I
recieve, and as I said It is launching the wrong matlab and I don't know how
change this.
Launching Matlab7p13
Warning: Unable to open display 'iconic'. You will not be able to display
graphics on the screen.
M A T L A B (R)
Copyright 1984-2011 The MathWorks, Inc.
R2011b (7.13.0.564) 32-bit (glnx86)
August 13, 2011
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.comhttp://www.mathworks.com/.
reading filled volume...
closing volume...
Undefined function 'fspecial' for input arguments of type 'char'.
Error in make_outer_surface (line 31)
Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file
'/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64
x86_64 x86_64 GNU/Linux
recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58 BST 2013
Thank you very much for your time and help,
Kind Regards,Linn
On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer
marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote:
Hi Linn,
Sorry for the delay in answering. The path has to be set directly in your
environment variable (the variable $PATH has to point to the correct version).
I need a few more details about what you tried and which OS you are using to be
able to help you.
If you are using mac, here is an example on how you can set the path in the
.shrc file:
setenv PATH $PATH:/Applications/MATLAB_R2013b.app/bin
You can also have a look at the following posts:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html
Let me know how it goes,
Marie
On Oct 22, 2013, at 2:41 AM, Linn Mittlestein
linnmit...@gmail.commailto:linnmit...@gmail.com
wrote:
Hi,
I am trying to compute lgi measures, and I think my problem lies in the fact
that the matlab path is not set correctly; it is calling an older version of
matlab however I need it to point to matlab2013b. I have tried numerous things
like changing the startup.m file, the .bashrc file and exporting the matlab
path, however It keeps calling another version of Matlab. Can someone please
tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
-- Forwarded message --
From: Linn Mittlestein linnmit...@gmail.commailto:linnmit...@gmail.com
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path problem
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein linnmit...@gmail.commailto:linnmit...@gmail.comDate:
Fri, Oct 18, 2013 at 1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Hi,
I am trying to compute lgi measures, and I think my problem lies in the fact
that the matlab path is not set correctly; it is calling an older version of
matlab however I need it to point to matlab2013b. I have tried numerous things
like changing the startup.m file, the .bashrc file and exporting the matlab
path, however It keeps calling another version of Matlab. Can someone please
tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
___
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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.
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[Freesurfer] fast_selxavg3.m - ERROR: design is ill-conditioned
I have two sets of identical blocks within each fMRI run, so conditions
{1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this
numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
...
ntptot = 687, nX = 136, DOF = 551
Saving X matrix to
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat
XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e.,
{1,2,3,4,5,6,7,8,9,10}
so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then
fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541
Saving X matrix to
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
XCond = 4.33238e+08 (normalized)
ERROR: design is ill-conditioned
1) why does nX increase by 10 in the 2nd case?
2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10
separate blocks?
The entire log file in the 2nd case is attached.selxavg3-sess log file
/usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess
-s subj008_10block -analysis improv.10blocks.sm05.lh
$Id: selxavg3-sess,v 1.60 2011/12/09 20:03:03 greve Exp $
uid=8240(preciado) gid=8240(preciado) groups=8240(preciado),160(fsdev),1071(birn),1107(fddev),1576(tbi)
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Wed Oct 23 11:37:06 EDT 2013
preproc-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -a improv.10blocks.sm05.lh -nolog
--
preproc-sess logfile is /dev/null
--
$Id: preproc-sess,v 1.50 2013/01/22 22:08:44 greve Exp $
preciado
setenv FREESURFER_HOME /usr/local/freesurfer/dev
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/preproc-sess
-s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -a improv.10blocks.sm05.lh -nolog
Wed Oct 23 11:37:06 EDT 2013
instem f
mc 1 f fmcpr
stc 1fmcpr fmcpr.siemens
sm 0
mask 1 brain
subj008_10block Template -
mktemplate-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -nolog -update
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:06 EDT 2013
Detected input format at nii
subj008_10block Update not needed
Run: 014
Wed Oct 23 11:37:06 EDT 2013
subj008_10block 014 Update not needed
Run: 016
Wed Oct 23 11:37:06 EDT 2013
subj008_10block 016 Update not needed
Run: 018
Wed Oct 23 11:37:07 EDT 2013
subj008_10block 018 Update not needed
Wed Oct 23 11:37:07 EDT 2013
mktemplate-sess completed
subj008_10block Mask
mkbrainmask-sess -maskstem brain -fsd bold -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -nolog -update
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:07 EDT 2013
subj008_10block Update not needed for session-level mask
subj008_10block Update not needed for run 014 mask
subj008_10block Update not needed for run 014 meanval
subj008_10block Update not needed for run 016 mask
subj008_10block Update not needed for run 016 meanval
subj008_10block Update not needed for run 018 mask
subj008_10block Update not needed for run 018 meanval
Wed Oct 23 11:37:07 EDT 2013
mkbrainmask-sess done
subj008_10block Registration -
register-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -nolog -update
--
register-sess logfile is /dev/null
--
Wed Oct 23 11:37:07 EDT 2013
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
cd /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/register-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -nolog -update
freesurfer-Linux-centos6_x86_64-dev-20131015
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:07 EDT 2013
Run: 014
Re: [Freesurfer] Projecting voxel intensities to a surface file
Sorry. I meant to do that. Original Message From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Arash Nazeri arashnaz...@aol.com Sent: Wed, Oct 23, 2013 8:25 am Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file Hi Arash can you cc the list on this type of email so that others can answer? Particularly Matt Glasser! I suspect that they have already run bbregister, but I'm not sure. cheers Bruce On Wed, 23 Oct 2013, Arash Nazeri wrote: Hi Bruce, Thanks for your response. I think this will do the trick generally, is it also possible to apply mri_vol2surf to the Human Connectome Project preprocessed files, or should I rerun the recon-all? In the HCP dataset, the surface files are in the gifti format and the diffusion images are already registered to the structural volumes. Based on the documentations it seems that mri_vol2surf is hard-wired for outputs generated from recon-all. Cheers, Arash -Original Message- From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Arash Nazeri arashnaz...@aol.com Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tue, Oct 22, 2013 10:17 pm Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file Hi Arash Yes. Register the surface to the volume with bbregister, then use mri_vol2surf to do the sampling Cheers Bruce On Oct 22, 2013, at 12:13 PM, Arash Nazeri arashnaz...@aol.com wrote: Dear all, I'm new to the freesurfer. I want to project surrounding cortical voxel values (intensities) from a given map (e.g. mean diffusivity map in a nifti format) to a surface file (e.g. mid-cortical surface in a gifti fromat) to generate scalar maps like ?h.thickness for group-wise statistics. Can this be carried out using freesurfer commands? Cheers, Arash ___ 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.
[Freesurfer] skull striping error question
Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha ___ 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] skull striping error question
Subha, The erroneous skullstripping will not affect your volume estimates as long as the surfaces look good. Maritza On Wed, 23 Oct 2013, Subhabrata Chaudhury wrote: Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha ___ 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] skull striping error question
Even the Supratentorial volume ? Supratentorial volume includes some structures outside the surfaces ? Thanks Subha - Original Message - From: Bruce Fischl Sent: 10/23/13 01:13 PM To: Subhabrata Chaudhury Subject: Re: [Freesurfer] skull striping error question You should be fine if the surfaces aren't affected by the remaining skull Bruce On Wed, 23 Oct 2013, Subhabrata Chaudhury wrote: Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha 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.
Re: [Freesurfer] skull striping error question
You should be fine if the surfaces aren't affected by the remaining skull Bruce On Wed, 23 Oct 2013, Subhabrata Chaudhury wrote: Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha ___ 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 statistics
Hi Lucia - The columns NVoxels Volume_mm3 in the mri_segstats output are the volumes of each of the structures in the aparc+aseg, so those columns have nothing to do with the path. The last few columns, Mean StdDev Min Max Range, are related to the values in path.pd.nii.gz. Hope this helps, a.y On Wed, 23 Oct 2013, Lucia Billeci wrote: Dear Anastasia, I tried the command you suggested me and i obtained the output I attach to the mail. I would like to ask you if I understood well shot it means. In this case left uncinatus connects the following cortex areas: ctx-lh-fusiform ctx-lh-inferiortemporal ctx-lh-lateralorbitofrontal ctx-lh-medialorbitofrontal ctx-lh-middletemporal ctx-lh-rostralanteriorcingulate ctx-lh-superiortemporal ctx-lh-temporalpole ctx-lh-insula and for each area I have the volume of the path. Is it correct? Thanks Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 18/ott/2013, alle ore 17:32, Anastasia Yendiki ha scritto: Hi Lucia - You can probably do that with mri_segstats. Try something like: mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz And similarly for any other pathway. See the mri_segstats help for more usage info. Let me know if this gives you what you need. a.y On Fri, 18 Oct 2013, Lucia Billeci wrote: Thanks Anastasia, this is useful for visualization. But to construct a table with for each tracts the parcellation regions that it connects do I need to look at the image? Lucia On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote: Hi Lucia - You can look at the tracula output over the cortical parcellation and subcortical segmentation in the individual's diffusion space like this: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv dpath/merged_avg33_mni_bbr.mgz Hope this helps, a.y On Fri, 18 Oct 2013, Lucia Billeci wrote: Dear Anastasia and all, how can I understand which are the region of the brain in which the brain base been parecellated that each tract generated by TRACULA connect? For example if I look at the left uncinate fascicles how can I know which are the ROIs of the statistical output from the cortical parcellation that it connects? Thanks Lucia On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote: Hi Anastasia, thanks for you answer. Now I have understood the meaning of that parameter. Best regards Lucia On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: Hi Lucia - It's how many sample paths were drawn to produce the probability distribution of the path (path.pd.nii.gz). It depends on the configuration parameters (nsample, nkeep), so it'll be the same if these configuration parameters are the same. Hope this helps, a.y On Mon, 14 Oct 2013, Lucia Billeci wrote: Dear all, I noticed that in the TRACULA statistics output files (pathstats.overall.txt) the variable Count that should indicate the number of sample paths in the WM tract is the same for all the computed tract. Could anyone tell me why this happen? Thanks a lot Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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
Re: [Freesurfer] Subject processing difference between computers
Thanks Ed. This is consistent with the differences we are seeing as well. The two super computers are very different platforms so it makes sense. I think we'll have to reprocess all cases for ongoing studies on the newer super computer in this case. Not the answer I was hoping for, but what I was expecting. Thanks again for the information. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ed Gronenschild Sent: Wednesday, October 23, 2013 9:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subject processing difference between computers see http://dx.plos.org/10.1371/journal.pone.0038234 On 22 Oct 2013, at 18:18, freesurfer-requ...@nmr.mgh.harvard.edumailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 2 Date: Tue, 22 Oct 2013 16:15:44 + From: West, John D. jdw...@iupui.edumailto:jdw...@iupui.edu Subject: [Freesurfer] Subject processing difference between computers To: freesurfer freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 793d43fe7976404cb5e172709ab1f4081123f...@iu-mssg-mbx102.ads.iu.edumailto:793d43fe7976404cb5e172709ab1f4081123f...@iu-mssg-mbx102.ads.iu.edu Content-Type: text/plain; charset=us-ascii Hello. We are moving our processing from an older super computer to a new one here at Indiana University. Preliminary testing is showing a significant difference between final summary stats results between subjects processed on the old system versus the new. The version of freesurfer on both systems is identical. Comparing the logs of the same subject run on both systems, I've found that the differences seem to start with the mri_watershed function specifically the main basin size. For the same subject we find: Old computer: main basin size=22667431830 voxels, voxel volume =1.000 = 22667431830 mmm3 = 22667431.936 cm3 New computer: main basin size=22208239350 voxels, voxel volume =1.000 = 22208239350 mmm3 = 22208239.616 cm3 As you can see they are very different. My theory is this is propagating through the rest of the process and giving us different summary stats at the end. I should note that both aseg and aparc stats are affected. I am also enclosing the logs for both runs as well as the differences found through the diff command (this is a lot parse through as even time stamp differences are picked up). Essentially what I am trying to find out is if these differences we are noticing are typical when changing computers and if not what could be causing these differences that I may not be picking up on. Thanks for the help. -John -- next part -- A non-text attachment was scrubbed... Name: recon-all.new.log Type: application/octet-stream Size: 451586 bytes Desc: recon-all.new.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20131022/fe052ee6/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: recon-all.old.log Type: application/octet-stream Size: 450567 bytes Desc: recon-all.old.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20131022/fe052ee6/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: recon-all.diff.log Type: application/octet-stream Size: 319424 bytes Desc: recon-all.diff.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20131022/fe052ee6/attachment-0002.obj ___ 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-sim with conjunction maps but without pre-cached data
Hi, I have a question regarding cluster size thresholding using mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made with mri_concat. The analyses that serve as input to the conjunction map are done on a custom surface template. If I want to run mri_glmfit-sim, how would that work? I obviously do not have precached data. Thanks, Caspar ___ 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_surf2surf error - 'could not determine type of...'
Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: *mri_surf2surf --srcsubject fsaverage \* *--srcsurfval lh.Yeo2011_17Networks_N1000.annot \* *--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh* I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \* *--o outfile.nii.gz --hemi lh --subject HS_001 \* *--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity* Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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] mri_surf2surf error - 'could not determine type of...'
The full error msg is not in the subject line. My guess is that the lh. in front of Yeo in the srcsurfval is causing the problem On 10/23/2013 03:17 PM, Paul Beach wrote: Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: /mri_surf2surf --srcsubject fsaverage \/ /--srcsurfval lh.Yeo2011_17Networks_N1000.annot \/ /--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh/ I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \/ /--o outfile.nii.gz --hemi lh --subject HS_001 \/ /--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity/ Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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] Problem generating volume stats with hippocampal segmentation script
Hi, I'm experiencing a problem when running the automated hippocampal subfield segmentation script. Unfortunately, I have been unable to determine the cause of the error. After reconstructing all participant data with the -hippo-subfields flag, I ran the kvlQuantifyHippocampalSubfieldSegmentations.sh script. The script seems to be working fine, generating subfield values for all participants until the very end when it attempts to generate the stat tables (I think). At this point, I receive the following error: /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt I've copied some output and the error message below, including the last participant in our folder it runs through before attempting to generate volume stats. Thanks for any help you can offer! Best Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Labhttp://www.psychiatry.wisc.edu/abercrombie/ 6001 Research Park Blvd. Madison, WI 53719 edubwa...@gmail.com Relevant information: FREESURFER_HOME: /Applications/freesurfer Current working dir ran command: /Applications/freesurfer/subjects/CORTMR/recon Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.4.0 x86_64 Command line ran: kvlQuantifyHippocampalSubfieldSegmentations.sh Output/Error (after seemingly generating hippocampal subfield values for all participants): ... cd 228/ Quantifying subject 228/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt cd .. Quantifying subject 228/ right Doing right side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4_DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt cd .. cd .. cd fsaverage/ Quantifying subject fsaverage/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt ___ 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] mri_surf2surf error - 'could not determine type of...'
Apologies: the full error message was: '*could not determine type of lh.Yeo2011_17Networks_N1000.annot*' I tried your suggestion of removing the hemispheric designation in front of 'Yeo' and I'm getting the same error - - the same occurs if I remove the '.annot' at the end. *mri_surf2surf --srcsubject fsaverage \* *--srcsurfval Yeo2011_17Networks_N1000.annot \* *--trgsubject HS_001 --trgsurfval Yeo_17Network_native.annot --hemi lh* *ERROR: could not determine type of Yeo2011_17Networks_N1000* Thoughts? Cheers, Paul On Wed, Oct 23, 2013 at 3:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The full error msg is not in the subject line. My guess is that the lh. in front of Yeo in the srcsurfval is causing the problem On 10/23/2013 03:17 PM, Paul Beach wrote: Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: /mri_surf2surf --srcsubject fsaverage \/ /--srcsurfval lh.Yeo2011_17Networks_N1000.annot \/ /--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh/ I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \/ /--o outfile.nii.gz --hemi lh --subject HS_001 \/ /--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity/ Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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] mri_surf2surf error - 'could not determine type of...'
try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of --srcsurfval cheers Bruce On Wed, 23 Oct 2013, Paul Beach wrote: Apologies: the full error message was: 'could not determine type of lh.Yeo2011_17Networks_N1000.annot' I tried your suggestion of removing the hemispheric designation in front of 'Yeo' and I'm getting the same error - - the same occurs if I remove the '.annot' at the end. mri_surf2surf --srcsubject fsaverage \ --srcsurfval Yeo2011_17Networks_N1000.annot \ --trgsubject HS_001 --trgsurfval Yeo_17Network_native.annot --hemi lh ERROR: could not determine type of Yeo2011_17Networks_N1000 Thoughts? Cheers, Paul On Wed, Oct 23, 2013 at 3:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The full error msg is not in the subject line. My guess is that the lh. in front of Yeo in the srcsurfval is causing the problem On 10/23/2013 03:17 PM, Paul Beach wrote: Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: /mri_surf2surf --srcsubject fsaverage \/ /--srcsurfval lh.Yeo2011_17Networks_N1000.annot \/ /--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh/ I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \/ /--o outfile.nii.gz --hemi lh --subject HS_001 \/ /--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity/ Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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] mri_surf2surf error - 'could not determine type of...'
That worked like a charm. Thanks! On Wed, Oct 23, 2013 at 5:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of --srcsurfval cheers Bruce On Wed, 23 Oct 2013, Paul Beach wrote: Apologies: the full error message was: 'could not determine type of lh.Yeo2011_17Networks_N1000.**annot' I tried your suggestion of removing the hemispheric designation in front of 'Yeo' and I'm getting the same error - - the same occurs if I remove the '.annot' at the end. mri_surf2surf --srcsubject fsaverage \ --srcsurfval Yeo2011_17Networks_N1000.annot \ --trgsubject HS_001 --trgsurfval Yeo_17Network_native.annot --hemi lh ERROR: could not determine type of Yeo2011_17Networks_N1000 Thoughts? Cheers, Paul On Wed, Oct 23, 2013 at 3:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The full error msg is not in the subject line. My guess is that the lh. in front of Yeo in the srcsurfval is causing the problem On 10/23/2013 03:17 PM, Paul Beach wrote: Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: /mri_surf2surf --srcsubject fsaverage \/ /--srcsurfval lh.Yeo2011_17Networks_N1000.**annot \/ /--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh/ I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.**HS_001.annot \/ /--o outfile.nii.gz --hemi lh --subject HS_001 \/ /--temp $SUBJECTS_DIR/HS_001/mri/orig.**mgz --identity/ Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/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/**freesurferhttps://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/**compliancelinehttp://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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ 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] freeview invalid drawable
Hi, When trying freeview command (see below) from the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the bert data too. What does invalid drawable mean? [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/ABU/surf/rh.pial:annot=aparc:edgecolor=red 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Thank you, Elissa ___ 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] freeview invalid drawable
You can just ignore this warning message on Mac. Best, Ruopeng On Oct 23, 2013, at 8:52 PM, Elissa McIntosh mcintosh.eli...@gmail.com wrote: Hi, When trying freeview command (see below) from the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the bert data too. What does invalid drawable mean? [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/ABU/surf/rh.pial:annot=aparc:edgecolor=red 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Thank you, Elissa ___ 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.
