[Freesurfer] .mgh to .label ??
Hello All, How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is there an automated way other than drawing ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] .mgh to .label ??
Hi Ri, I think you can use mri_cor2label with flag --id set to 1. Sita. On Mon, 16 May 2011, Ritobrato Datta wrote: Hello All, How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is there an automated way other than drawing ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] two questions
Hi there, First the simple question - is there a way to run mris_anatomical_stats on all my subjects at once generating a single output file? Second - actually comprised from several questions: when looking a the unthresholded group analysis on cortical thickness (in the averaged space), the distribution of negative and positive z values is not necessarily normal. i.e., the range of negative values maybe be 0 to -5, and the range of positive values 0 to +3. 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. 3. Is there a way to set FDR separately for positive and negative values? thanks ilana Ilana Hairston hairstons...@gmail.com * Our ignorance is not so vast as our failure to use what we know. —M. King Hubbert, peak oil prophet ___ 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] visualization after cluster correction
Hi Heidi, I think this is what you need: csdbase.sig.cluster.mgh - the sig volume corrected for multiple comparisons on a cluster-wise basis. The value at each voxel is the -log10(p), where p is the pvalue of the cluster at that voxel. If that voxel does not belong to a cluster, its value will be 0. This info can be found by running mri_glmfit-sim with the --help option doug Jacobs H (NP) wrote: Hi FreeSurfers, This is more a visualization question. I did the cortical thickness analyses on my data and compared my two groups statistically. After that I ran the mri_glmfit-sim to correct for multiple comparisons using the cluster correction. When I visualize the results, each cluster has its own color. However, I would like to present the original sig.mgh file (where each vertex has received a significance value according to the color table) minus the clusters that did not survive the correction. How should I do that? Thank you very much! Best regards Heidi * * *Heidi Jacobs, MSc.* /PhD student Faculty of Health, Medicine and Life Sciences/ /School for Mental Health and Neurosciences/ /Alzheimer Center Limburg/ /Division Cognitive Neuropsychiatry and Clinical Neurosciences /_h.jac...@maastrichtuniversity.nl mailto:h.jac...@maastrichtuniversity.nl _www.maastrichtuniversity.nl http://www.maastrichtuniversity.nl/ Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 *Note: the email addresses have changed!* *Please consider your environmental responsibility before printing this 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 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_surfcluster and the color table
Hi Elisa, how was the slt file created? Can you send it and the summary file to me (don't send to the group). doug Elisa Golfinopoulos wrote: Hi all, I wanted to follow-up on my previous e-mail, which may have been a bit too vague. I am using the command: mri_surfcluster --in ./osgm/sig.mgh --subject average --surf inflated --annot slt --sign abs --csd ../csd/mc-z.abs-osgm.csd --sum ./osgm/summaryfile.txt --o ./osgm/cluster_peaks.o --ocn ./osgm/cluster_number.ocn --sd /speechlab/2/egolfino/srate/nipype/fsdata This command runs without error. The slt annotation file is found in the right directory and read, but when I display the summary text file I find that for each cluster the label under Annot is NOT FOUND. This is not the case when I use mri_surfcluster, but substitute slt with aparc. That is, when I use this substitution, in the summary text file under Annot Freesurfer's labels are generated. I notice that when I run mri_surfcluster with aparc, after the annotation file is read, the colortable is read from the annotation file and the terminal indicates colortables with 36 entries read (originally /autofs/space/terrer_001/users/nicks/freesurfer/average/colortable_desikan_killany.txt). The color table is not read when I run mri_surfcluster with the slt annotation file. I am assuming that our slt annotation file is missing information in the header regarding the corresponding color table and I am wondering if there is a way for me to generate a link between the annotation file and the color table? Is it possible for me to set the color table information in the annotation file or set the color table information externally so mri_surfcluster knows which label corresponds with each id? Any suggestions would be greatly appreciated. Thanks so much for your help. Cheers, Elisa P.S.: I am using the 5th version of Freesurfer for a 64 bit machine. On Mon, May 2, 2011 at 5:33 PM, Elisa Golfinopoulos egolf...@bu.edu mailto:egolf...@bu.edu wrote: Hi, I am trying to use an annotation file that was created from a parcellation scheme developed in my lab with mri_surfcluster. However, it's unclear to me how I can set the corresponding color table for this annotation file either locally or globally. mri_surfcluster doesn't seem to have a --ctab or --colortable argument. Is there a way to set the color table as an environment variable and would this be an appropriate workaround or is it the case that the color table is a fixed setting for mri_surfcluster? Your help is greatly appreciated. Cheers, Elisa -- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181 tel:617.353.6181 -- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181 tel:617.353.6181 ___ 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] discrepancy between p-values computed from t.nii and those stored in sig.nii
Those residuals are actually whitened, but there is still a problem in that you need to include the whitening matrix in the equation for the t ratio below. I don't know any easy way to do it from there. You can save the unwhitened residuals with -svres-unwhitenen, then compute the average of the residuals, then compute a whitening matrix (eg, assuming AR1), then recompute rvar and the t. But this is not perfect either. In reality, you should average the raw time courses and then do the whole analysis from scratch. doug Pablo Polosecki wrote: Hi Doug, I know I'm reviving an old question. It seems to me that the variance of the errors estimated the way you are proposing below (i.e. using the residuals provided by selxavg3-sess) is biased in the sense that the residuals are not whitened (i.e. they are not independent becasue there is a temporal correlation), and that I could make an incorrect inference because of that. Am I right? If so, could you perhaps suggest a way of correcting for that? Thank you very much, Pablo On Fri, Nov 12, 2010 at 11:03 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The residuals are not saved by default, but you can tell selxavg3-sess to save them by adding the -svres flag. By variance I mean the temporal variance of the mean waveform of the residuals. The t that you want is given by: t = ces/sqrt(rvar * C'*inv(X'*X)*C) where ces is the average ces over the ROI, the rvar is the variance described above, X is the design matrix, and C is the contrast matrix. Both of these are in the X.mat matrix. doug Pablo Polosecki wrote: Oh, thank you. I am a little bit lost now. Could you clarify a little bit more for me? Could you tell where the residuals are stored? By variance of the residuals you mean variance across voxels in the ROI? What is the efficiency of the contrast? On Thu, Nov 11, 2010 at 12:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That's actually not the right way to do it either. You need to get the residuals for the ROI, average the residuals, compute the variance of the average residual. Then divide this by the efficiency for the contrast, then take the sqrt() of this number. This is the standard error of the ces. Then compute the average ces over the ROI. The t is then the average ces/standard error. doug Pablo Polosecki wrote: Well, that is bad (beacuse there is a bug) and good (because now it is known) at the same time. I wanted to estimate a p-value for a group of voxels of interest for a certain contrast in my analysis. Instead of averaging the p values for these voxels, I thought it would make more sense to calculate the average t statistic for the voxels and then estimate the p-value for the group of voxels myself using tcdf function in matlab. So, I guess I need the t values for that, unless I can think of a workaround, which so far I couldn't. Best, Pablo On Thu, Nov 11, 2010 at 11:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Pablo, you have found a bug in FSFAST in which the values in the t.nii file are actually the sqrt of the p-values. I have fixed it in our code base and it will be in the next version. Do you actually need the t-values? thanks! doug Pablo Polosecki wrote: I understand the X.mat contains the variable DOF which tells me the degrees of freedom for the analysis, right? In my case it is 5915. This is what I get when I load X.mat into a structure named 'x': x = DoSynth: 0 UseFloat: 0 SynthSeed: -1 flac0: [1x1 struct]
Re: [Freesurfer] Load normalized thickness into Matlab
Hi Rene, you can load these with MRIread.m doug René Besseling wrote: Dear all, I'd like to analyse some Freesurfer outputs in Matlab. I know it is possible to load ./surf/lh.thickness into Matlab using read_curv, but is it also possible to load normalized (and smoothed) thickness maps, i.e. thickness maps registered to fsaverage, for vertex-wise comparison? I thought these normalized maps would be called something like ./surf/lh.curv.fwhm10.fsaverage, but I only find files like ./surf/lh.curv.fwhm10.fsaverage.mgh (note the .mgh extension) which dont work with read_curv. Am I missing something? Best regards, René ___ 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] Segmentation Fault
Hi Chinduri, is this still happening? I can't replicate. doug Chindhuri Selvadurai wrote: Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 Fri May 13 12:21:58 EDT 2011 Run: 012 Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC - mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null --- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 --- ** --- --- Motion Correcting Run 012 --- --- ** --- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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] sliver problem with tksurfer over VNC
Hi all, I am experiencing the infamous sliver problem in tksurfer over VNC. I tried solving it by installing VirtualGL, but it doesn't work, I get the following error message: [VGL] WARNING: VirtualGL attempted and failed to obtain a Pbuffer-enabled [VGL]24-bit visual on the 3D X server :0. If the application [VGL]subsequently fails, then make sure that the 3D X server is configured [VGL]for 24-bit color and has accelerated 3D drivers installed. Window type not found! My xorg.conf shows 24 bit color depth. I am running Scientific Linux 5.4 on a Dell PE R905 with embedded ATI ES1000 video controller. It might be that the ATI ES1000 doesn't support hardware acceleration, it is a rack server. Does anybody have experience with this issue? Pointers? Cheers, Diederick ___ 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] [Major Upgrade] - iSurf Brainview 3.0.0
Today it was released the version 3.0.0 of iSurf Brainview, it's a major version release for IPad, IPhone and IPod Touch. Major New Features - Quiz for Brain structures (you can take a Quiz with 10 random questions about structure locations. The current database has more than 40 questions) - Select the brain structure by name - You have a list of available structures. Minor Changes - Visual Improvements - Memory usage improvement - Paper of Destrieux, C. - Versioning As usual suggestions and feedbacks are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 A personal note: Some residents in Radiology of our med school found the quiz challenging. I think it can be a very good tool to teach neuroanatomy in MRI - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ 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] two questions
Hi Ilana, I'll let the first question to the FS experts to answer. For the second: 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? Even if the effect exists, your experiment wasn't able to detect it as significant, since nothing survived the multiple testing correction you used. Most scientific journals wouldn't accept conclusions based on non-significant results, despite how compelling the hypothesis might be. 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. The p-values are in the files sig.mgh, in subdirectories of the qdec directory where the results of the analyses were stored. There are multiple ways to open and a suggestion is to convert to ASCII using the -c option of mris_convert, then open in Octave/Matlab with dlmread. 3. Is there a way to set FDR separately for positive and negative values? The plain answer is no, because for the FDR procedure to work, it's necessary that the p-values under the null are uniformly distributed between 0 and 1 (from the definition of p-values). If you drop part of your distribution, then the p-values are no longer distributed like that. It turns out, however, that in some particular cases, part of the distribution does not actually exist (see Self Liang, J Am. Stat Assoc, 1987 for some cases, particularly the Cases 5 and 7). A workaround is to divide the q by a constant that depends on the fraction of the distribution that known to be missing (e.g., for Case 5, instead of q=0.05, one could use q=0.025 to obtain the same 5% of false discoveries). However, these particular cases I believe don't apply to your scenario, so please, refrain from applying FDR separately only on positives or negatives. There is also a second reason for not applying FDR separately: for each set (positive and negative), the number of tests would be reduced, on average, by half, alleviating the multiple testing problem and making, on average, twice as easy for results to survive the threshold, inflating the amount of false discoveries, something undesired. Hope this helps! All the best, Anderson On 05/16/2011 09:53 AM, Ilana Hairston wrote: Hi there, First the simple question - is there a way to run mris_anatomical_stats on all my subjects at once generating a single output file? Second - actually comprised from several questions: when looking a the unthresholded group analysis on cortical thickness (in the averaged space), the distribution of negative and positive z values is not necessarily normal. i.e., the range of negative values maybe be 0 to -5, and the range of positive values 0 to +3. 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. 3. Is there a way to set FDR separately for positive and negative values? thanks ilana Ilana Hairston hairstons...@gmail.com * Our ignorance is not so vast as our failure to use what we know. —M. King Hubbert, peak oil prophet ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_segstats error
Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 sysname Darwin hostname Fernanda-Palhanos-Mac-Pro.local machine i386 user fernandapalhano atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 ) ERROR: could not open stats/aseg.stats for writing Any ideas? Thanks, Fernanda ___ 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_segstats error
does the stats directory exist? doug Fernanda Palhano wrote: Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 sysname Darwin hostname Fernanda-Palhanos-Mac-Pro.local machine i386 user fernandapalhano atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 ) ERROR: could not open stats/aseg.stats for writing Any ideas? Thanks, Fernanda ___ 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] mri_segstats error
And do you have write permissions? Can you touch stats/aseg.stats doug Fernanda Palhano wrote: Yes. [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats] fernandapalhano% ls aseg.statslh.aparc.a2009s.statslh.supramarg.stats rh.aparc.a2009s.statswmparc.stats lh.aparc.a2005s.statslh.aparc.stats rh.aparc.a2005s.statsrh.aparc.stats Fernanda On Mon, May 16, 2011 at 4:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: does the stats directory exist? doug Fernanda Palhano wrote: Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 sysname Darwin hostname Fernanda-Palhanos-Mac-Pro.local machine i386 user fernandapalhano atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 ) ERROR: could not open stats/aseg.stats for writing Any ideas? Thanks, Fernanda ___ 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 Fax: 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 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] two questions
Hi Ilana, Normality isn't a requirement for FDR to work. However, if the distribution of your statistic isn't normal **under the null hypothesis**, neither follows t, F or any other well known parametrizable distribution, then you have to obtain p-values in a different way, not from the cdf/pdf of these distributions. Most likely you'd have to use permutations. But do you have any evidence that your cortical thickness measurements are not normal after regressing out your model? The histogram that appears in qdec window tells you the frequency of the statistics across space for all the vertices. This is not the same as the distribution of the residuals, nor of the statistic for each vertex if the same experiment were to be repeated many, many times. You could apply a normality test to each vertex using the residuals of the GLM. I wouldn't bother much with that, though. I see no reason why thickness measurements wouldn't be normal. All the best! Anderson On 05/16/2011 03:18 PM, Ilana Hairston wrote: thanks! very helpful. not to be argumentative, but if my Z distribution is not normal, is there meaning to FDR? On May 16, 2011, at 2:08 PM, Anderson Winkler wrote: Hi Ilana, I'll let the first question to the FS experts to answer. For the second: 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? Even if the effect exists, your experiment wasn't able to detect it as significant, since nothing survived the multiple testing correction you used. Most scientific journals wouldn't accept conclusions based on non-significant results, despite how compelling the hypothesis might be. 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. The p-values are in the files sig.mgh, in subdirectories of the qdec directory where the results of the analyses were stored. There are multiple ways to open and a suggestion is to convert to ASCII using the -c option of mris_convert, then open in Octave/Matlab with dlmread. 3. Is there a way to set FDR separately for positive and negative values? The plain answer is no, because for the FDR procedure to work, it's necessary that the p-values under the null are uniformly distributed between 0 and 1 (from the definition of p-values). If you drop part of your distribution, then the p-values are no longer distributed like that. It turns out, however, that in some particular cases, part of the distribution does not actually exist (see Self Liang, J Am. Stat Assoc, 1987 for some cases, particularly the Cases 5 and 7). A workaround is to divide the q by a constant that depends on the fraction of the distribution that known to be missing (e.g., for Case 5, instead of q=0.05, one could use q=0.025 to obtain the same 5% of false discoveries). However, these particular cases I believe don't apply to your scenario, so please, refrain from applying FDR separately only on positives or negatives. There is also a second reason for not applying FDR separately: for each set (positive and negative), the number of tests would be reduced, on average, by half, alleviating the multiple testing problem and making, on average, twice as easy for results to survive the threshold, inflating the amount of false discoveries, something undesired. Hope this helps! All the best, Anderson On 05/16/2011 09:53 AM, Ilana Hairston wrote: Hi there, First the simple question - is there a way to run mris_anatomical_stats on all my subjects at once generating a single output file? Second - actually comprised from several questions: when looking a the unthresholded group analysis on cortical thickness (in the averaged space), the distribution of negative and positive z values is not necessarily normal. i.e., the range of negative values maybe be 0 to -5, and the range of positive values 0 to +3. 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. 3. Is there a way to set FDR separately for positive and negative values? thanks ilana Ilana Hairston hairstons...@gmail.com * Our ignorance is not so vast as our failure to use what we know. —M. King Hubbert, peak oil prophet ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] mri_segstats error
yes, that is fine. doug Fernanda Palhano wrote: Doug, I have another question about doing a volumetric group analysis. I used the command: asegstats2table --subjects V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30 V31 V32 --tablefile asegstats_new.txt --common-segs To extract volume information for all my subjects. I'm interested in use Left-Hippocampus and Right-Hippocampus to perform my group analysis. Is it correct just import the columns data ( Left-Hippocampus and Right-Hippocampus) in some statistical software? Thanks a lot, Fernanda On Mon, May 16, 2011 at 4:25 PM, Fernanda Palhano nandapalh...@gmail.com mailto:nandapalh...@gmail.com wrote: Doug, Actually, the file aseg.stats already exists. I think I only have to use asegstats2table http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table to combine the stats from all my subjects. Fernanda On Mon, May 16, 2011 at 4:15 PM, Fernanda Palhano nandapalh...@gmail.com mailto:nandapalh...@gmail.com wrote: Yes. [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats] fernandapalhano% ls aseg.statslh.aparc.a2009s.stats lh.supramarg.statsrh.aparc.a2009s.statswmparc.stats lh.aparc.a2005s.statslh.aparc.stats rh.aparc.a2005s.statsrh.aparc.stats Fernanda On Mon, May 16, 2011 at 4:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: does the stats directory exist? doug Fernanda Palhano wrote: Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 sysname Darwin hostname Fernanda-Palhanos-Mac-Pro.local machine i386 user fernandapalhano atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 ) ERROR: could not open stats/aseg.stats for writing Any ideas? Thanks, Fernanda ___ 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 Fax: 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 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
Re: [Freesurfer] Segmentation Fault
Hi, I am experiencing the same problem. When I try to do the motion correction on fmri data it stops with a segmentation fault in mri_convert. This used to work until this week. Best Marcus On 13.05.2011 12:48, Chindhuri Selvadurai wrote: Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 Fri May 13 12:21:58 EDT 2011 Run: 012 Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC - mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null --- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 --- ** --- --- Motion Correcting Run 012 --- --- ** --- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints? ___ 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] Segmentation Fault
OK, I've verified and fixed this. It will be in dev in the next build (probably overnight). Are you using dev? doug Marcus Belke wrote: Hi, I am experiencing the same problem. When I try to do the motion correction on fmri data it stops with a segmentation fault in mri_convert. This used to work until this week. Best Marcus On 13.05.2011 12:48, Chindhuri Selvadurai wrote: Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 Fri May 13 12:21:58 EDT 2011 Run: 012 Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC - mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null --- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 --- ** --- --- Motion Correcting Run 012 --- --- ** --- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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 -- 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] freeview: creating ROIs, measuring volume
Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI. How can I select my ROI in three planes in freeview so that I can eventually get a volume output in mm^3? Someone here suggested I trace by hand on every slice in every view, but that can't be the way it's done, is it (please say it isn't)? Thanks! Lynette -- Lynette M. Silva, M.S. Doctoral Candidate Department of Psychology University of New Mexico ___ 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: creating ROIs, measuring volume
When you say tracing an ROI by hand in freeview, did you fill it or just traced the outline? In any case, you will need to do this on each slice by hand. However, there're various options and tools in freeview that may help speed up the process dramatically. Ruopeng On 5/16/11 5:12 PM, Lynette Silva wrote: Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI. How can I select my ROI in three planes in freeview so that I can eventually get a volume output in mm^3? Someone here suggested I trace by hand on every slice in every view, but that can't be the way it's done, is it (please say it isn't)? Thanks! Lynette ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
PPJ, Hi, mri_info /space/incoming/ga_2010.nii shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview or tkmedit, the brain seems 'squashed', as if there is a slice gap. do you know the details of how this was acquired? N. On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints? ___ 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] freeview: creating ROIs, measuring volume
Thanks Ruopeng, I tried tracing the outline with the freehand tool, and I also tried setting waypoints around the surface area of my ROI. What tools would you recommend? Thanks again! Lynette On Mon, May 16, 2011 at 3:46 PM, Ruopeng rpw...@nmr.mgh.harvard.edu wrote: When you say tracing an ROI by hand in freeview, did you fill it or just traced the outline? In any case, you will need to do this on each slice by hand. However, there're various options and tools in freeview that may help speed up the process dramatically. Ruopeng On 5/16/11 5:12 PM, Lynette Silva wrote: Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI. How can I select my ROI in three planes in freeview so that I can eventually get a volume output in mm^3? Someone here suggested I trace by hand on every slice in every view, but that can't be the way it's done, is it (please say it isn't)? Thanks! Lynette ___ 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. -- Lynette M. Silva, M.S. Doctoral Candidate Department of Psychology University of New Mexico ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freeview: creating ROIs, measuring volume
You can try use the flood-fill tool to fill the ROI you outlined. On 5/16/11 5:58 PM, Lynette Silva wrote: Thanks Ruopeng, I tried tracing the outline with the freehand tool, and I also tried setting waypoints around the surface area of my ROI. What tools would you recommend? Thanks again! Lynette On Mon, May 16, 2011 at 3:46 PM, Ruopengrpw...@nmr.mgh.harvard.edu wrote: When you say tracing an ROI by hand in freeview, did you fill it or just traced the outline? In any case, you will need to do this on each slice by hand. However, there're various options and tools in freeview that may help speed up the process dramatically. Ruopeng On 5/16/11 5:12 PM, Lynette Silva wrote: Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI. How can I select my ROI in three planes in freeview so that I can eventually get a volume output in mm^3? Someone here suggested I trace by hand on every slice in every view, but that can't be the way it's done, is it (please say it isn't)? Thanks! Lynette ___ 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] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
The images are: 0.5 x 0.5 x 1.0 Can mri_convert fix it or should I edit the Nifti header? 2011/5/16 Nick Schmansky ni...@nmr.mgh.harvard.edu PPJ, Hi, mri_info /space/incoming/ga_2010.nii shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview or tkmedit, the brain seems 'squashed', as if there is a slice gap. do you know the details of how this was acquired? N. On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints? ___ 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.
