[Freesurfer] problem mri_convert
Dear FreeSurfers, On one of our Linux machines we encounter the following error message when calling mri_convert: /lib64/libz.so.1: no version information available (required by mri_convert) /usr/lib64/libstdc++.so6: version GLIBCXX_3.4.11 not found (required by mri_convert) Mri_convert has worked before without any problem. Any advices how to resolve this would be very welcome! Best Regards, Ruthger ___ 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] Extract values in ROI to ascii file
Dear Freesurfers, I am using mris_convert to obtain per vertex thickness values in an ascii file. What I would like to do is to limit the requested area to a certain region of interest using a label file. Is this possible? (analogous to mris_anatomical_stats where a label flag can be given?). Thank you very much in advance all the best! Ruthger ___ 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] including a vertex-specific covariate in mri_glmfit
Dear Freesurfers, I have a question about mri_glmfit for surface analyses. I have until now used covariates which provided one value for each subject (e.g., Age) but was wondering if it is possible to use covariates that have different values for each vertex. I would like to perform a GLM analysis of thickness with another surface-based measure as covariate. For example, Salat et al. (2009) analysed the effect of age on GWR (ratio of gray matter - white matter) and regressed out thickness at each vertex along the cortical surface (i.e., an individual model for each vertex utilizing the thickness and contrast). My question is: is this possible in mri_glmfit as applied in Freesurfer and if so, how to do it? If not, are there other tools that might help me out? Reference: Salat, Lee, van der Kouwe et al. (2009). Age-associated alterations in cortical gray and white-matter signal intensity and gray to white matter contrast. NeuroImage, 48, 21-8. http://www.ncbi.nlm.nih.gov/pubmed/19580876 Thank you very much in advance for your time and help! Ruthger Righart ___ 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] Name external disk not recognized
Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger ___ 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] Name external disk not recognized
Yes, works!!! Thank you Ruthger Righart Le 2014-10-30 15:36, Douglas Greve a écrit : can you make a symbolic link (ln -s) to the disk and then reference the symlink instead of the direct path? On 10/30/14 10:33 AM, Righart, Ruthger wrote: Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PhD position | Technische Universität München, Munich, Germany
PhD position in multiple sclerosis research Department of Neurology, Technische Universität München, Munich, Germany TUM-NIC, Neuroimaging Center, Munich, Germany The Department of Neurology of the Technische Universität München offers a PhD position in systems neuroscience research of Multiple Sclerosis. The project aims to investigate structural correlates of disability and biomarker patterns in patients with multiple sclerosis (MS) using MR imaging techniques. The candidate will investigate cortical pathology and lesion pathology in MS using state-of-the-art neuroimaging techniques. Applicants should have finished a university degree in medicine, psychology, biology, computer science or other relevant disciplines. Candidates should have strong analytical and organizational skills and prior experience with large cohort patient datasets is an advantage. Previous experience in analysis of structural/functional MR images (e.g., Freesurfer/FSL, SPM) is highly desired. Basic programming skills in for example Matlab or Unix shell scripting are a plus but not strictly required. Candidates who lack the aforementioned skills should have a strong motivation to develop these skills during their training. We are searching for candidates who are able to work independently and who have demonstrated excellent presentation and writing skills. The applicant will be expected to interact and collaborate with colleagues from different disciplines. Salary is according to the German TVöD. The position is available from January. The position is initially available for two years, the second year contingent on satisfactory progress. Extension beyond two years may be possible. Neuroimaging scanning facilities (MRI 3T scanner) and computer infrastructure are entirely available at the TUM Neuroimaging Center (TUM-NIC). Candidates may contact Prof Dr. Mark Mühlau (mueh...@lrz.tum.de) or Dr. Ruthger Righart (righ...@lrz.tum.de) for more detailed information. Applications including a letter of motivation and CV should be addressed to Prof. Dr. Mühlau by Email: mueh...@lrz.tum.de . ___ 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] Scatter plot after mri_glmfit
Hi All, In Tksurfer it is possible to view a scatter plot of a relationship analyzed by mri_glmfit, by File - Load Group Descriptor File (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization). Is this also possible in Freeview? I tried Tools - Plot FSGD Data, but that does not work. Best, Ruthger Righart ___ 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] T2 flag
Hi Bruce, Thank you very much for your prompt reply. It would be great if you could take a look. Would you need anything more than the original t1.nii and t2.nii? Best, Ruthger Le 2014-04-14 16:18, Bruce Fischl a écrit : Hi Ruthger, I've only tested the deformation on T2-space, and mostly with a flair inversion pulse, so it is probably the case that it doesn't work well with your sequence. If you want to upload the data I'll try to take a look, but it probably won't be soon sorry Bruce On Mon, 14 Apr 2014, Righart, Ruthger wrote: Dear Freesurfers, I have run several subjects using the -T2pial flag, to correct for dura. For several subjects the pial surface was badly positioned after the -T2pial flag was used (these errors did not occur when the flag was not used, in the same subject, see PDF, left vs right panel). I was wondering if adding this flag might be problematic in some patient groups, like cerebrovascular disease or multiple sclerosis, with regard to T2 (hyperintense) lesions. Best, Ruthger ___ 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] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist
Hi All, mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf). Thank you very much in advance for your help! All the best, Ruthger ___ 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] removal oblique sforms
Dear Freesurfers, To obtain an accurate volume-surface alignment of Freesurfer surfaces in Caret, it is advised that oblique sforms should be removed from the header of the t1w images. I tried to remove the sform (using sform_code='0' and qform='1') and changed the nii header using fslcreatehd. However, something seems to go wrong, as my thickness data of the same subject are different than the thickness data from the original t1w images. In addition, alignment in Caret is still poor. I am puzzled and I would be happy to have your suggestions about removing sforms. Thank you very much in advance! FS 5.3. was run on a Linux machine x86_64. Ruthger ___ 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] tkmedit background color
Dear Freesurfer experts, I am trying to find out how to change the background color of tkmedit. Is there a possibility to change the background color from black to white, just for display purposes? (to avoid laborious photoshop work). Best Regards, Ruthger Righart ___ 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] tksurfer crashes
Dear Freesurfer experts, I have a problem with Tksurfer. Whereas this worked previously fine it suddenly crashes every time I try to start it. This happens with every subject or fsaverage. A similar problem was reported before with similar terminal output but unfortunately I could not find a solution to this problem in the mailing list. Any suggestions are welcome! Ruthger Righart Hi Michelle, hmmm, no idea. Do you want to upload the the subject and we'll see if we can replicate the problem? Do you have enough memory on that machine? Bruce On Mon, 19 Mar 2012, Michelle Umali wrote: Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects tksurfer ld07 lh inflated subject is ld07 hemiis lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07) ___ 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] surface does not match
Dear Freesurfers, I analyzed a dataset with FS 5.1 but upon loading the data in tksurfer I get the following error: mrisReadTriangleFile(/.../surf/lh.sphere.reg): surface doesn't match /.../surf/lh.inflated The same error occurs when I run mris_preproc as a step before GLM analyses (mri_glmfit). A similar problem was described in the mailing list and offered the possibility to resolve this with the following command: recon-all -s subjid -make all This command only runs at the moment for a few of my subjects (I am at the moment waiting for the results of these analyses). For the majority of my subjects having the same error in mrisReadTriangleFile this command does not run. For those, it seems that the command -make all is not recognized. Does anyone know why it does not run or is there an alternative solution in FS 5.1. for this problem? Thank you very much in advance for your help! Ruthger Righart ___ 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] SupraTentorial Volume question
Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume? 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? Any help or suggestions is very much appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] Volume-based stream: SupraTentorial Volume and Lesion-Mask
Dear All, We are making Volume-based analyses and I have a few questions. 1. The SupraTentorial BrainVolume is indicated in the aseg.stats. I found an explanation on http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats about the SupraTentorial Vol., but checking the formula by summing up Cortex + CorticalWhiteMatter + SubCortGray I do not arrive at the exact value of SupraTentorial as indicated in the aseg.stats; for some of my subjects this value is higher, for some lower. What could cause these differences except from differences between voxel-based measures (i.e., SubCortGray) and surface-based measures? Is CSF and ventricle volume already subtracted from this value? Please see below copied the aseg.stats file for one subject: Cortex 448248.101786 + CorticalWhiteMatter 404368.03125 + SubCortGray 215645 = 1068261.13. This differs from the supratentorial value indicated in aseg.stats, which is 1218507.78. 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? If there are any lesions in structures, I would like to subtract lesion volume these structures that are listed in aseg.stats. Best Regards, Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /Applications/freesurfer/ASegStatsLUT.txt --subject 1008 # # SUBJECTS_DIR /Network/Xgrid/freesurfer_M0HL # subjectname 1008 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 225756.920309, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 222491.181478, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 448248.101786, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 198684.625000, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 205683.406250, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 404368.031250, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 215645.00, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 663893.101786, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1218507.775726, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1882094.762769, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2010/12/01 23:41:35 # ColorTable /Applications/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2010/08/15 20:35:08 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2010/12/01 18:52:15 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2010/12/01 18:52:15 # Excluding Cortical Gray and White Matter # ExcludeSegId 0 2 3 41 42 # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 45 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 4416544165.0 Left-Lateral-Ventricle19.7155 16.3746 0.89.89. 2 5 2806 2806.0 Left-Inf-Lat-Vent 38.3263 15.7951 0.83.83. 3 7 1365713657.0 Left-Cerebellum-White-Matter 81.6728 7.880419. 104.85. 4 8 5824758247.0 Left-Cerebellum-Cortex66.2938 9.300914. 102.88. 5 10 7895 7895.0
[Freesurfer] mri_label2label problem
Dear Freesurfers, I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I have some problems in that the target label shows little holes while the location of the target label seems to correspond rather well with the source label. Checking these holes backward to the source subject using the function tools/send to subject in tksurfer ... brings the saved point in the source label. I think this problem has been reported in the list before (see copy below) but unfortunately I do not find a solution that removes the holes. In my case I see this now and then both for ROIs that I drew myself in tksurfer but also pre-defined ROIs that were already there (e.g., rh.G_and_S_cingul-Mid-Ant.label). What might go wrong here? I am using --regmethod surface and trgsurf white. I wondered further how one may check how well mri_label2label worked for each subject. Is there a way to test that source and target labels have the same location in terms of for example gyri and sulci? Are there cases that mri_label2label cannot work? Thank you very much for your help, any suggestions appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15125.html Re: [Freesurfer] Mri_label2label problem? Douglas N Greve Tue, 21 Sep 2010 06:47:09 -0700 what does the original label look like? Can you convert one of the predefined labels (eg, lh.V1.label) to see if the same thing happens? doug Pye, Brandon (NIH/NIMH) [F] wrote: Hey guys, We are using mri_label2label to convert a label created from a cluster (using mri_surfcluster) from an average subject to each individual subject. We have 6 individual labels that we are converting. All of the analysis is done using surface data. I use the command in the generalized form listed below: Mri_label2label -srcsubject fsaverage -srclabel cluster1.label -trg subject Subject -trglabel Subject_cluster1.label -regmethod surface -hemi lh 5 of the 6 labels transfer well, but a 6th label translated to the correct anatomical location, but the number of labeled vertices is greatly reduced after the translation. This problem persists across all subjects. There doesn't appear to be much interior to the label, just a lot of the outline of the label (i.e. If the outline of the label is yellow and the interior is blue, I see a lot of yellow and not much blue, as if there are a bunch of small islands). The region on them most inferior part of the lateral surface approximately where the temporal and occipital lobes meet. Any ideas what might be going on? Thanks, - Brandon Pye Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 402-3893 Fax: (301) 402-0921 brandon@nih.gov ___ 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] What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?
Dear All, I am working with the volume-based stream in Freesurfer and I have a question about what is the difference between the volumes given for Cortical-white-matter and Cerebral-white-matter? How are the volumes calculated for both in Freesurfer? Is it the difference of including or not including the subcortical gray matter and ventricles in the calculation? I have read previous mailings ( e.g. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15449.html ) but I am still confused what is the difference between these measures. Thank you very much in advance for your help! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] FW: What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?
Hi Allison, Thank you very much for your help! I am using v5.0.0. Is the surface of the white-matter (from the surface-based stream) used here to calculate the volume in CorticalWhiteMatterVol and is this why I have sub-millimeter values here? This value is in fact different from the value that can be calculated in mri_segstats for cerebral-white-matter using the command mri_segstats --seg aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --sum test1.stats. Is this because segstats makes the calculation here in voxels? Is it therefore better to take the value from CorticalWhiteMatterVol which would take the white-matter surface into account? Best, Ruthger From: Allison Stevens [astev...@nmr.mgh.harvard.edu] Sent: Friday, May 20, 2011 2:56 PM To: Righart, Ruthger Dr. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer? Which version of FreeSurfer are you using? In the more recent versions, they are the same. Cortical White Matter is all the white matter contained within the white surface minus the subcortical gray matter and ventricles, etc. On May 20, 2011, at 7:37 AM, Righart, Ruthger Dr. ruthger.righ...@med.uni-muenchen.de wrote: Dear All, I am working with the volume-based stream in Freesurfer and I have a question about what is the difference between the volumes given for Cortical-white-matter and Cerebral-white-matter? How are the volumes calculated for both in Freesurfer? Is it the difference of including or not including the subcortical gray matter and ventricles in the calculation? I have read previous mailings ( e.g. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15449.html ) but I am still confused what is the difference between these measures. Thank you very much in advance for your help! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] Cortical thickness of a Volume-defined ROI: Reshaping dimensions
Dear Freesurfers, I would like to map my subject thickness data to the fsaverage subject, following ROI analyses, as described under step 4: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Before step 4, tksurfer showed me that registration from MNI to Freesurfer space of my ROI went well! After that I would like to get thickness data using mri_segstats (step 5). However, Freesurfer indicates that the dimensions of my segmentation image (23406 x 1 x 7) are different from the dimensions of my input image (27307 x 1 x 6), and using mri_info suggests that sth seems to have gone wrong in step 4. I have searched in the Freesurfer archives and I understood that 23406 x 1 x 7 are the correct dimension values and followed the advise to use --reshape in the fourth step. This does however not change the dimensions (it still indicates in the Freesurfer output: Reshaping 6 (nvertices = 163842) which I guess should be Reshaping 7). Any suggestions to solve this problem of different dimensions are very much appreciated! Best Regards, Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] Lobe mapping, based on the Desikan-Killiany Atlas
Dear Freesurfers, I would like to do Lobe mapping, based on the Desikan-Killiany atlas, see http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. I was wondering if there is a reason why the banksts is not included in the list under temporal lobe. My first guess is because this is a sulcus, but I would like to be sure what is the reason. Thank you very much for your suggestions! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] Setting lesion voxels
Dear Freesurfers, I would like that surface analyses (i.e., cortical thickness) are not confounded by subcortical lesions in patients. Freesurfer provides a work-around in its release notes ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), which is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and in aseg.mgz to 77 and then run recon-all -autorecon2-cp (see copy text underneath). As I have lesion masks of every patient I thought it would be best to automatize this step. In that case, I would like to bring mask images with white matter lesions of these patients in the same (freesurfer) space as my T1.mgz, with dimensions 256 x 256 x 256, spacing 1 x 1 x 1., and after that set the lesions to the aforementioned values. Is there a possibility to bring lesion mask of these patients in the same space as T1.mgz in freesurfer? I inspected the function bbregister and mri_convert but could not find a solution here. Any help or suggestions are appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp ___ 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] segfault
Dear Sir/Madam, I am a new user of freesurfer and had the following error when I tried in tkmedit tool to make a snapshot of the volume. Please find below the contents of the file .xdebug_tkmedit Best Regards, Ruthger Righart ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... tkmedit started: Tue Sep 21 14:22:11 2010 tkmedit.bin 1001 1001-M36-T1.mgz $Id: tkmedit.c,v 1.341.2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5 $ Set user home dir to /Network/Servers/isd06363.isd.med.uni-muenchen.de/Shared Items/homefolder/rrighart Set subject home dir to /Volumes/ext_rrighart/CADASILData/1001 Using interface file /Applications/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Segfault Verifying volume xDebug stack (length: 4) 03: Volm_SaveToSnapshot( this=0x38c6600 ) 03: Verifying volume 02: SnapshotVolume () 02: Saving snapshot 01: main() 01: Entering main loop 00: 00: ___ 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.
