[Freesurfer] Repost: fsgd file
Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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] Memory allocation problem trac-all -prior
-- Forwarded message -- From: Rui Lavrador ruilavra...@gmail.com Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador 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. -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com ___ 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] multiple correction
On 07/06/2012 10:00 PM, Meng Li wrote: Hi, freesurfer expert, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? correct 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? If you are drawing conclusions from both hemispheres then you need to use .025 3) And what is the difference between fdr and mc-z correction? mc-z uses a cluster-wise correction and controls the rate of false positive clusters. FDR is voxel-wise and controls the false discovery rate, which is the number of false positives relative to the total number of positives (as compared to the number of false positives relative to the total number of tests). doug Thanks, Meng ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] qdec
Hi Carolina, the FWHM is the full-width/half-maximum and indicates how much smoothing you have. This is surface-based smoothing, not volume based, and it can be difficult to compare to volume based smoothing as is done in fMRI. The surface-based smoothing can be larger because you don't have to worry about smoothing in white matter and CSF or jumping across a sulcus as you would at higher levels of volume-based smoothing. There is no answer to the actual level of smoothing you need because it depends on how big the blob is. 10mm is typical. fMRI analysis often has this level of smoothing in the volum.e doug On 07/07/2012 02:44 PM, carolina.mr wrote: Hello, In the qdec analysis the default smoothing factor is 10. What does it mean? For other technics such as fMRI we generally use a lower smoothing factor (~3 or lower). What would happen if I low down the FWHM? Thank you, Carolina ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Ribbon
You can try mris_volmask \ --label_left_white 2 --label_left_ribbon 3 \ --label_right_white 41 --label_right_ribbon 42 \ --save_ribbon $subjid doug On 07/08/2012 01:18 PM, Matt Glasser wrote: Hi Bruce, He just needs the grey matter part of a typical ribbon.mgz volume. He lost some of his recon-all folder. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday, July 08, 2012 12:17 PM To: Colin Reveley Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Ribbon Hi Colin what is the representation you want in the end? You can also fill the interior of the surfaces using mris_fill then do some boolean algebra on the results of e.g. the white and pial interiors. cheers Bruce On Sun, 8 Jul 2012, Colin Reveley wrote: Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to register FLAIR to T1?
Often with FLAIR there is not enough gray-white contrast to run the registration. Try using the pial surface instead, with -surf pial --t1 This tells it to use the pial surface as a boundary. The --t1 is needed because the intensity should go from bright to dark. Let me know if that does not fix the problem. doug On 07/10/2012 11:58 AM, Bruce Fischl wrote: glad to hear it :). You may need to repost (and possibly upload your data) On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions. Cheers, Ed On 10 Jul 2012, at 16:57, Bruce Fischl wrote: Hi Ed, sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization. cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, Unfortunately, this has no effect. Ed On 10 Jul 2012, at 16:40, Bruce Fischl wrote: Hi Ed you are using -t2, right? You can also try -init-header cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi Bruce, It is slightly better but still displacements in all directions and rotations too exist. Ed On 10 Jul 2012, at 16:13, Bruce Fischl wrote: try -init-spm cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote: Hi, I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap). The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows: bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 and inspected the result with tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1. It makes hardly any difference if instead of --t1 --t2 as contrast setting was used. Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR? (FreeSurfer v4.5.0, MacOSX 10.5) Cheers, Ed ___ 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 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Measuring total cortical volume
In the aseg.stats file, there will be these values # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 218425.204942, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 212261.052152, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 430686.257094, mm^3 does this work for you? doug On 07/16/2012 03:17 AM, Emelie Andersson wrote: Hello, We have a some doubts about how to measure the total cortical volume. Is it recommendable to use GM = pial surface - white matter? Hope to hear from You, Best regards Emelie ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c
Thanks Doug! New version of mri_segstats is working fine for images with small voxels (1mm3). --Masaya On 07/16/2012 09:43 AM, Douglas N Greve wrote: Hi Masaya, you are correct. I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux Can you test it out? It also fixes the partial volume computation problem. thanks! doug On 07/06/2012 02:23 PM, Masaya Misaki wrote: I've posted a question about a strange behavior of mri_segstats if voxel size isn't 1 mm3 and --pv option is used. I found a reason of this problem in the source code of mri_segstats.c (release_5_1_0 branch was checked out from read-only CVS source-code repository) In mri_segstats.c the return value from MRIvoxelsInLabelWithPartialVolumeEffects is used as the number of voxels; nhits = MRIvoxelsInLabelWithPartialVolumeEffects (seg, pvvol, StatSumTable[n].id, NULL, NULL); vol = nhits*voxelvolume; However, MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c returns volume (e.g. volume += vox_vol; or volume += vox_vol * pv;), not the number of voxels. nhits value is adjusted by voxel volume in mri_segstats.c (vol = nhits*voxelvolume), so that the voxelvolume (vox_vol) is multiplied twice. The volume reported by mri_segstats, therefore, is too small if the voxel volume is less than 1 mm^3 or too large if the voxel volume is larger than 1 mm3. Note that this is not a problem when voxel volume is conformed to 1 mm3 (default option in recon-all). I think many of FreeSurfer programs do not support high-resolution ( 1mm3) image without conforming to 1 mm3 voxel, but could you fix the problem of mri_segstats? I want to use mri_segstats with partial volume correction for high-resolution MRI image. Thank you, --Masaya On 06/26/2012 08:40 AM, Masaya Misaki wrote: Hello all, I found volume size reported by mri_segstats is changed very much depending on voxel size when partial volume correction (--pv option) is used. The difference was much larger than that can be explained by the difference of image resolution. (mri_segstats version is 1.75.22 2011/4/27 in FreeSurfer v5.1.0) When I performed segmentation for high-resolution image (voxel size = 0.5 mm^3), I found all volumes of segmented regions in aseg.stats was too small; about 8 times smaller than that was estimated from 1mm^3 conformed image. So I tested the effect of voxel size on mri_segstats. At first, recon-all was run with conforming 1mm^3 voxel (default option). Then aseg.mgz and norm.mgz were conformed to small voxel size, and mri_segstats was applied to the conformed files: mri_convert aseg.mgz aseg_cs05.mgz -cs 0.5 rt nearest mri_convert norm.mgz norm_cs05.mgz -cs 0.5 mri_segstats --seg aseg_cs05.mgz --pv norm_cs05.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --nonempty --excludeid 0 --sum aseg_cs05.stats (these are just for testing the effect of voxel size, not for actual analysis) All volumes reported in aseg_cs05.stats (for 0.5mm^3 voxel) was about 8 times smaller than aseg.stats (for 1mm^3 voxel). So the reported volume was scaled with the same ratio as the voxel size. Same effect was observed when voxel size was conformed to larger one (e.g. 1.5mm^3); reported volumes were about 3 times larger than those for 1mm^3-voxel. The number of voxels in the segmented regions (Nvoxels column in aseg.stats) were similar across different voxel sizes while voxel sizes are different. When --pv option was not used, the reported volumes were almost the same across different voxel sizes. So the partial volume correction in mri_segstats seems to depend on voxel size. Can I fix this with some missed options or shouldn't I use --pv option for the image with voxel size other than 1mm^3? thanks, -- Masaya Misaki Ph.D. ___ 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] Repost: fsgd file
Hi Heidi, how exactly do you want to draw a conclusion? The slopes for the different variables may be very different because the variables have a different scale. tksurfer scatter plot is made to look at a cortical variable vs a continuous variable. If you want to look at a scatter plot of your continuous variables, why not just do it in matlab or excel? doug On 07/16/2012 04:47 AM, Jacobs H (NP) wrote: Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Flip brain
Hi Tadeu, I have updated the files. The only difference is that the mcc file below is now ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz doug On 07/10/2012 09:25 AM, Tadeu Kubo wrote: Hi Dear FS experts, Doug sent these links, but I can't download them. Do you have the new links? Download these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linux Thank you. Regards, Tadeu ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] qdec - ERROR: CSDread():
Does /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd exist and do you have read permission? doug On 07/10/2012 09:20 AM, Natalia h wrote: Dear expert, I got an error while clicking the Monte Carlo simulation in qdec. I am using Mac 10.6 and qdec version 1.4, freesufer 5.1 Have no clue why it always gives this error in the terminal: mri_surfcluster --in /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/sig.mgh --csd /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd --mask /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/mask.mgh --cwsig /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.mgh --vwsig /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.vertex.mgh --sum /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.summary --ocn /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.mgh --oannot /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.annot --csdpdf /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.pdf.dat --annot aparc --cwpvalthresh 0.05 --surf white ERROR: CSDread(): could not open /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd ERROR! Very appreciate for the help ! Thank you in advance, Natalia ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Coordinate Transformations
Hi, I'm working on a project project comparing the cortical thickness in epileptic patients to the corresponding brain area of a control subject. To do this, I have been trying to transform the patient RAS coordinates to talairach coordinates and then transforming the talairach coordinates into the RAS coordinates of the control. In doing this, I have two problems. First, when I use the transformation matrix provided in the free surfer subject folder (multiply RAS coordinate by transformation matrix in /mri/transforms/talairach.xfm) the coordinates seem to map to similar although not exactly the same area. Second, what is the best way to transform a set a talairach coordinates to RAS coordinates? Thank you for your help, Jared ___ 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] Repost: fsgd file
Hi Doug, Thanks for your reply. Both scores are on the same scale (z-transformed). But I would like to see whether there is a differential effect on cortical thickness. Do you think the contrast I defined was correct? And do I understand it correctly that what you suggest is the following: warp the clusters to individual space and extract the values for SPSS (or excel)? Thanks! Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: maandag 16 juli 2012 18:17 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Repost: fsgd file Hi Heidi, how exactly do you want to draw a conclusion? The slopes for the different variables may be very different because the variables have a different scale. tksurfer scatter plot is made to look at a cortical variable vs a continuous variable. If you want to look at a scatter plot of your continuous variables, why not just do it in matlab or excel? doug On 07/16/2012 04:47 AM, Jacobs H (NP) wrote: Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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
Re: [Freesurfer] ROI from left to right hemi - cortical thickness
Dear Doug, thanks for your answer. I guess I got confused by the output of the interhemispheric registration. So, to be sure I understood correctly: are you suggesting that I should 1) run mri_label2label --srcsubject suj1 --trgsubject suj1/xhemi --srclabel $SUBJECT_DIR/suj1/label/lh.mylabel.label --trglabel $SUBJECT_DIR/suj1/xhemi/label/lh.mylabel.label --regmethod surface --surfreg sphere --hemi lh 2) copy the newly created label /suj1/xhemi/label/lh.mylabel.label to suj1/label/rh.mylabel.label and calculate stats from that one? Thanks again! Have a nice day, Irene Le lundi 16 juillet 2012 à 10:49 -0400, Douglas N Greve a écrit : Hi Irene, what are the instructions you are following? If you have mapped the lh.roi to the LH of the xhemi subject (making it the RH), then you can copy it to subject/label/rh.roi and run the normal stats. doug On 07/09/2012 04:31 AM, Irene Altarelli wrote: Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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] ROI from left to right hemi - cortical thickness
that looks right except --surfreg sphere should be --surfreg fsaverage_sym.sphere.reg Where did you get those instructions? Did I send them out before? doug On 07/16/2012 01:32 PM, Irene Altarelli wrote: Dear Doug, thanks for your answer. I guess I got confused by the output of the interhemispheric registration. So, to be sure I understood correctly: are you suggesting that I should 1) run mri_label2label --srcsubject suj1 --trgsubject suj1/xhemi --srclabel $SUBJECT_DIR/suj1/label/lh.mylabel.label --trglabel $SUBJECT_DIR/suj1/xhemi/label/lh.mylabel.label --regmethod surface --surfreg sphere --hemi lh 2) copy the newly created label /suj1/xhemi/label/lh.mylabel.label to suj1/label/rh.mylabel.label and calculate stats from that one? Thanks again! Have a nice day, Irene Le lundi 16 juillet 2012 à 10:49 -0400, Douglas N Greve a écrit : Hi Irene, what are the instructions you are following? If you have mapped the lh.roi to the LH of the xhemi subject (making it the RH), then you can copy it to subject/label/rh.roi and run the normal stats. doug On 07/09/2012 04:31 AM, Irene Altarelli wrote: Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Coordinate Transformations
Have you looked at this page http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug On 07/16/2012 12:43 PM, jmd33 wrote: Hi, I'm working on a project project comparing the cortical thickness in epileptic patients to the corresponding brain area of a control subject. To do this, I have been trying to transform the patient RAS coordinates to talairach coordinates and then transforming the talairach coordinates into the RAS coordinates of the control. In doing this, I have two problems. First, when I use the transformation matrix provided in the free surfer subject folder (multiply RAS coordinate by transformation matrix in /mri/transforms/talairach.xfm) the coordinates seem to map to similar although not exactly the same area. Second, what is the best way to transform a set a talairach coordinates to RAS coordinates? Thank you for your help, Jared ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Repost: fsgd file
That contrast is correct. If you run mri_glmfit-sim, it will extract the data for each subject and cluster and save it in a text file in the contrast directory. It is better to do it this way instead of mapping the ROIs back to the individual. Look at mri_glmfit-sim --help doug On 07/16/2012 12:52 PM, Jacobs H (NP) wrote: Hi Doug, Thanks for your reply. Both scores are on the same scale (z-transformed). But I would like to see whether there is a differential effect on cortical thickness. Do you think the contrast I defined was correct? And do I understand it correctly that what you suggest is the following: warp the clusters to individual space and extract the values for SPSS (or excel)? Thanks! Heidi Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: maandag 16 juli 2012 18:17 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Repost: fsgd file Hi Heidi, how exactly do you want to draw a conclusion? The slopes for the different variables may be very different because the variables have a different scale. tksurfer scatter plot is made to look at a cortical variable vs a continuous variable. If you want to look at a scatter plot of your continuous variables, why not just do it in matlab or excel? doug On 07/16/2012 04:47 AM, Jacobs H (NP) wrote: Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] annot 2 label file conversion
Can you send your command line and the full terminal output? doug On 07/11/2012 09:39 AM, Bruce Fischl wrote: Hi Arnaud this question may need to wait for Doug to return. If you don't get an answer in a couple of days try reposting, and please include your exact command line and screen output and FS version. cheers Bruce On Wed, 11 Jul 2012, Arnaud Messé wrote: Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I only found 770 label file. For another parcellisation scheme, I found 325 entries in annot file and 496 label files... These findings are consistent across several subjects. So my question is how mri_annotation2label processes annot file? and how to find correspondence between annot and label files? Any advice would be greatly appreciate, ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Clusterwise correction for multiple comparisons
It does not seem like it should take that much time. You might try this program ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mcsim.linux This is what I use to create the cached results that we distribute. You can use the cached results unless you have a different mask. If you use mri_mcsim, there will be a few extra steps (not just a replacement for mri_glmfit-sim). Let me know if you get that far. doug On 07/11/2012 06:50 AM, Ed Gronenschild wrote: Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the csd file I can read that it still has more than 1000 steps to go. Is it possible that it takes that much time? Cheers, Ed ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] ROI functional anatomical cross
You can create a binary mask of the ROI, then use mri_mask to mask out the non-ROI part from the fMRI. does that work? doug On 07/11/2012 11:25 AM, Huiting Liu wrote: Hello, I'm trying to do an ROI analysis that crosses the group-level functional activation with specific anatomical structures. Currently the clusters found for our group-level functional activation are too large and need to be separated into many structures. Is there a command I could use that would cross the group level map with each cortical structure generated by freesurfer's recon-all? Thanks. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] the make_average_subject without aparc.annot
I don't remember what I sent out before, but you can try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface doug On 07/11/2012 03:37 PM, Leon wrote: Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] parcellations to fmri space
I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks. Chris On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug On 07/06/2012 12:02 PM, Christopher Bell wrote: Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it. My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks! Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my Rube Goldberg approach. Chris ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] Splotchy labels after transformation from fsaverage to native
Hi, just wanted to bump this up since it looks like Doug is back.
On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom mwas...@stanford.eduwrote:
Hi,
I'm using mri_label2label to reverse normalize labels from fsaverage
space to the native surface.
I'm ending up with some splotchy-looking labels, for lack of a better
word. See what I mean here:
http://web.mit.edu/mwaskom/www/splotchy.png
I'm doing this normalization in a script with the following relevant
line, which seems to be what happens inthe BAlabes step of recon-all
mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label \
--srcsubject fsaverage --trgsubject ${subj} \
--trglabel label/$hemi.${roi}.label \
--regmethod surface --hemi $hemi
Any idea how I can avoid this splotchiness or, failing that, do a
closing on the label to clean up some of the noise?
Cheers,
Michael
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Re: [Freesurfer] parcellations to fmri space
So you want to make a particular label bigger (more surface area) on cortex? doug On 07/16/2012 02:51 PM, Christopher Bell wrote: I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks. Chris On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug On 07/06/2012 12:02 PM, Christopher Bell wrote: Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it. My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks! Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my Rube Goldberg approach. Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all
Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.___ 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] sum of WM and GM coming out to be bigger than ICV after recon-all
Hi Ayaz what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2) cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. ___ 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] Splotchy labels after transformation from fsaverage to native
There is not an easy/good way to handle this situation. The way it works
is that it goes through each point in the source and finds the closest
vertex in the target. If the target is more densely sampled, then there
are some points in the target in the middle of the label that are not
the closest vertex to any label vertex in the source. It is hard to
figure out computationally whether an unlabeled point is in the middle
of the label or halfway around the brain. One thing that might work ok
is to save the output as a binary mask (--outmask), then smooth it a
little (mris_fwhm or mri_surf2surf), then re-binarize the mask
(mri_binarize), then convert it to a label (mri_cor2label --i
smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white --o
lh.label.yoursubject).
doug
On 07/16/2012 03:30 PM, Michael Waskom wrote:
Hi, just wanted to bump this up since it looks like Doug is back.
On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom mwas...@stanford.edu
mailto:mwas...@stanford.edu wrote:
Hi,
I'm using mri_label2label to reverse normalize labels from fsaverage
space to the native surface.
I'm ending up with some splotchy-looking labels, for lack of a better
word. See what I mean here:
http://web.mit.edu/mwaskom/www/splotchy.png
I'm doing this normalization in a script with the following relevant
line, which seems to be what happens inthe BAlabes step of recon-all
mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label \
--srcsubject fsaverage --trgsubject ${subj} \
--trglabel label/$hemi.${roi}.label \
--regmethod surface --hemi $hemi
Any idea how I can avoid this splotchiness or, failing that, do a
closing on the label to clean up some of the noise?
Cheers,
Michael
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--
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all
Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that? -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all Hi Ayaz what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2) cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. 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. The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Restart from somewhere in the middle of mri_ca_register
Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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] ROI functional anatomical cross
Hi Doug, Thank you, I think that will work. Right now my anatomical ROIs are in subject native space and I would like to register the third-level group (across subject) fmri activation map to subject native space as well before crossing the two. Is that possible? I have the anat2exf.register.dat files for each subjects's group feat (across runs) but I don't know how to do it for the third level? Thanks so much, Huiting On Mon, Jul 16, 2012 at 2:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: You can create a binary mask of the ROI, then use mri_mask to mask out the non-ROI part from the fMRI. does that work? doug On 07/11/2012 11:25 AM, Huiting Liu wrote: Hello, I'm trying to do an ROI analysis that crosses the group-level functional activation with specific anatomical structures. Currently the clusters found for our group-level functional activation are too large and need to be separated into many structures. Is there a command I could use that would cross the group level map with each cortical structure generated by freesurfer's recon-all? Thanks. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register
no, sorry : On Mon, 16 Jul 2012, Joshua Lee wrote: Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the 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] Restart from somewhere in the middle of mri_ca_register
not that I have any real hope lol - Josh On Mon, Jul 16, 2012 at 1:41 PM, Joshua Lee jki...@ucdavis.edu wrote: Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the 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] Restart from somewhere in the middle of mri_ca_register
Yeah I didn't think so..well my fault for trying to push 30 brains through at a time on just 24 cores and 24 Gigs of RAM, and all started within 10 minutes of each other..froze her up and locked others out. Ahh, well. Thanks Bruce and crew! - Josh On Mon, Jul 16, 2012 at 1:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: no, sorry : On Mon, 16 Jul 2012, Joshua Lee wrote: Is it possible/pracitcal? This is a long step, and unfortunately my analysis computer was rebooted in the middle of this step, and I was hoping to present the volumes tomorrow.. ouch. - Josh 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. ___ 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] recon-all for non-human primates failed and what to do next?
Hi, FreeSurfer experts. I have successfully used FreeSurfer to reconstruct monkey brains, but when I used the same scripts on chimpanzees, it failed miserably (see the attached figure). I tried several strategies, such as normalizing the wm.mgz to 110, but the scripts still did not work. Could someone tell me what other strategies I could use to make it work? Many thanks in advance! Leon ___ 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] Splotchy labels after transformation from fsaverage to native
Hmm, ok. Are there no functions for doing a dilation/erosion on a surface
label?
On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
There is not an easy/good way to handle this situation. The way it works
is that it goes through each point in the source and finds the closest
vertex in the target. If the target is more densely sampled, then there
are some points in the target in the middle of the label that are not
the closest vertex to any label vertex in the source. It is hard to
figure out computationally whether an unlabeled point is in the middle
of the label or halfway around the brain. One thing that might work ok
is to save the output as a binary mask (--outmask), then smooth it a
little (mris_fwhm or mri_surf2surf), then re-binarize the mask
(mri_binarize), then convert it to a label (mri_cor2label --i
smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white --o
lh.label.yoursubject).
doug
On 07/16/2012 03:30 PM, Michael Waskom wrote:
Hi, just wanted to bump this up since it looks like Doug is back.
On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom mwas...@stanford.edu
mailto:mwas...@stanford.edu wrote:
Hi,
I'm using mri_label2label to reverse normalize labels from fsaverage
space to the native surface.
I'm ending up with some splotchy-looking labels, for lack of a better
word. See what I mean here:
http://web.mit.edu/mwaskom/www/splotchy.png
I'm doing this normalization in a script with the following relevant
line, which seems to be what happens inthe BAlabes step of recon-all
mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label \
--srcsubject fsaverage --trgsubject ${subj} \
--trglabel label/$hemi.${roi}.label \
--regmethod surface --hemi $hemi
Any idea how I can avoid this splotchiness or, failing that, do a
closing on the label to clean up some of the noise?
Cheers,
Michael
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--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
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Re: [Freesurfer] Splotchy labels after transformation from fsaverage to native
Hi Michael,
yes, you can do this in tksurfer with a tcl script (labl_erode and
labl_dilate I believe). Not sure if there is a binary to do it, but it
would be pretty easy to write
Bruce
On Mon, 16 Jul 2012, Michael Waskom wrote:
Hmm, ok. Are there no functions for doing a dilation/erosion on a surface
label?
On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
There is not an easy/good way to handle this situation. The way
it works
is that it goes through each point in the source and finds the
closest
vertex in the target. If the target is more densely sampled,
then there
are some points in the target in the middle of the label that
are not
the closest vertex to any label vertex in the source. It is hard
to
figure out computationally whether an unlabeled point is in the
middle
of the label or halfway around the brain. One thing that might
work ok
is to save the output as a binary mask (--outmask), then smooth
it a
little (mris_fwhm or mri_surf2surf), then re-binarize the mask
(mri_binarize), then convert it to a label (mri_cor2label --i
smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white
--o
lh.label.yoursubject).
doug
On 07/16/2012 03:30 PM, Michael Waskom wrote:
Hi, just wanted to bump this up since it looks like Doug is
back.
On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom
mwas...@stanford.edu
mailto:mwas...@stanford.edu wrote:
Hi,
I'm using mri_label2label to reverse normalize labels from
fsaverage
space to the native surface.
I'm ending up with some splotchy-looking labels, for lack of a
better
word. See what I mean here:
http://web.mit.edu/mwaskom/www/splotchy.png
I'm doing this normalization in a script with the following
relevant
line, which seems to be what happens inthe BAlabes step of
recon-all
mri_label2label --srclabel
../fsaverage/label/${hemi}.${roi}.label \
--srcsubject fsaverage --trgsubject ${subj} \
--trglabel label/$hemi.${roi}.label \
--regmethod surface --hemi $hemi
Any idea how I can avoid this splotchiness or, failing that, do
a
closing on the label to clean up some of the noise?
Cheers,
Michael
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--
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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.
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Re: [Freesurfer] multiple comparisons correction
Dear professor, Thanks for your reply. You said that when drawing conclusions from both hemispheres then I need to use .025, but I found that in qdec interface, the default value of -cwpvalue is 0.05. So are they inconsistent? I also want to find a solution about an ERROR. I tried to run a cortical thickness analysis to look for differences between two groups (patients and controls) with regressing out the gender factor, the patients group have 1 female and 17 male, after analysis, I got the results. But when I add another continuous variable as covariate, I received the message: ERROR: matrix is ill-conditioned or badly scaled. Then I tried to change the gender composition the patients groups: 2 female/16 male, and the problem was solved. so is it right about what i did, or I need another way to solve this problem? Thanks, Best wishes Meng On 07/06/2012 10:00 PM, Meng Li wrote: Hi, freesurfer expert, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? correct 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? If you are drawing conclusions from both hemispheres then you need to use .025 3) And what is the difference between fdr and mc-z correction? mc-z uses a cluster-wise correction and controls the rate of false positive clusters. FDR is voxel-wise and controls the false discovery rate, which is the number of false positives relative to the total number of positives (as compared to the number of false positives relative to the total number of tests). doug Thanks, -- ___ 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.
