[Freesurfer] Is there any way of finding out RESEL number in the GLM output?
Hello Freesurfer users, I'd hope to know the RESEL number in my group GLM analysis data. I can calculate the number of vertices and also see the fwhm.dat in the ouput GLM folder, but I wonder if there is anyway of finding out RESEL size if freesurfer also provides that info like SPM does. -Glen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?
thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?
Hi Doug -- I copied and pasted the summary file below. It looks like mask.mgh was treated as volumetric image. Also I'm not sure how to interpret TableCol. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ # cmdline mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat # sysname Linux # hostname rage.uphs.upenn.edu # machine x86_64 # user gel # anatomy_type volume # # SegVolFile mask.mgh # SegVolFileTimeStamp 2013/06/05 14:50:24 # InVolFile /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area # InVolFileTimeStamp 2013/05/22 16:49:43 # InVolFrame 0 # Only reporting non-empty segmentations # 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 Mean # TableCol 5 FieldName Intensity Mean # TableCol 5 Units unknown # TableCol 6 ColHeader StdDev # TableCol 6 FieldName Itensity StdDev # TableCol 6 Units unknown # TableCol 7 ColHeader Min # TableCol 7 FieldName Intensity Min # TableCol 7 Units unknown # TableCol 8 ColHeader Max # TableCol 8 FieldName Intensity Max # TableCol 8 Units unknown # TableCol 9 ColHeader Range # TableCol 9 FieldName Intensity Range # TableCol 9 Units unknown # NRows 1 # NTableCols 9 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 8183781837.0 Seg0001 0.3836 0. 0.1297 1.1861 1.0563 On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Did you look in the summary file? If you have questions about that, can you send it? doug On 06/11/2013 11:34 AM, Glen Lee wrote: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: what is your full command line? On 6/11/13 10:04 AM, Glen Lee wrote: thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 tel:1%20%C2%A0%2081837%20%C2%**A081837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/**surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu
Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?
Got it. Thanks for the prompt answer! By the way, I tried mri_segstats with --accumulate flag, but it says option '--accumulate' is unknown. I don't seem to find it when I looked up mri_segstas --help either. On Tue, Jun 11, 2013 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Right, so in this case, the NVoxels column is the number of vertices, the Mean column is the average surface area of the vertices in the mask. You can force it to compute the total surface area by adding the --accumulate flag. Or you can multiple the mean by the number of vertices. doug On 06/11/2013 04:55 PM, Glen Lee wrote: Hi Doug -- I copied and pasted the summary file below. It looks like mask.mgh was treated as volumetric image. Also I'm not sure how to interpret TableCol. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ # cmdline mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat # sysname Linux # hostname rage.uphs.upenn.edu http://rage.uphs.upenn.edu # machine x86_64 # user gel # anatomy_type volume # # SegVolFile mask.mgh # SegVolFileTimeStamp 2013/06/05 14:50:24 # InVolFile /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area # InVolFileTimeStamp 2013/05/22 16:49:43 # InVolFrame 0 # Only reporting non-empty segmentations # 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 Mean # TableCol 5 FieldName Intensity Mean # TableCol 5 Units unknown # TableCol 6 ColHeader StdDev # TableCol 6 FieldName Itensity StdDev # TableCol 6 Units unknown # TableCol 7 ColHeader Min # TableCol 7 FieldName Intensity Min # TableCol 7 Units unknown # TableCol 8 ColHeader Max # TableCol 8 FieldName Intensity Max # TableCol 8 Units unknown # TableCol 9 ColHeader Range # TableCol 9 FieldName Intensity Range # TableCol 9 Units unknown # NRows 1 # NTableCols 9 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 8183781837.0 Seg0001 0.3836 0. 0.1297 1.1861 1.0563 On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Did you look in the summary file? If you have questions about that, can you send it? doug On 06/11/2013 11:34 AM, Glen Lee wrote: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --sum sum.dat On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: what is your full command line? On 6/11/13 10:04 AM, Glen Lee wrote: thanks Doug. it worked and I got the following result on which I have clarifying questions: -- Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 81837 81837 tel:1%2081837%20%2081837 tel:1%20%C2%A0%2081837%20%C2%**A081837 1) I'm assuming that voxel here refers to vertex since I'm submitting the surface data. 2) what does 'found 1 segmentations mean'? 3) the dimension is 81837mm^2, correct? On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_**sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o
[Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?
Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?
Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer 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_glmfit-sim error
Doug -- Sorry for asking your help again as I can't seem to resolve this on my own. I looked up the mri_glmfit-sim --help and added the path of csd file in the argument, but it still fails to find .csd file. Can you let me know once again what I did wrong? (see the command line below). mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim /csd/mc-z.negative.j001-osgm.csd --overwrite Also see the output below. Original mri_glmfit command line: cmdline mri_glmfit --y Bb_Bp_sm8_i6_n13_L.mgh --osgm --glmdir GLM --surf fsaverage_sym lh DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 5.124509 ERROR: cannot find any csd files On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: --no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug On 06/04/2013 09:11 AM, Glen Lee wrote: Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below: /2D/results/LH/GLM/csd ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this csd folder? Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite -Glen On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote: Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: You will need more like 1 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.**csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.**cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.**mgh --sum GLM/osgm/perm.abs.2.sig.**cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.**mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.**annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.**masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/**subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign
Re: [Freesurfer] mri_glmfit-sim error
Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below: /2D/results/LH/GLM/csd ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this csd folder? Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite -Glen On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote: Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You will need more like 1 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.00 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLowCWPHi NVtxs Annot ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
[Freesurfer] mri_glmfit-sim error
Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.00 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot ___ 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_glmfit-sim error
Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: You will need more like 1 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.00 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLowCWPHi NVtxs Annot ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to determine a smoothing kernel size for surface that is approx. equal to 4mm in volumetric data?
Hello Freesurfer users I'm trying to replicate my earlier findings in 3D space by warping the data into surface using freesurfer. Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm wondering what size of smoothing kernel for 2D would be equivalent to 4mm for volumes. Any help would be greatly appreciated. Glen ___ 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] warning after running mris_fwhm
Hello FreeSurfer experts, I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices. Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 =0) may be critical. If anyone has any idea/ suggestions, please help. -Glen mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4 --i rabold4_0065_sym_L.mgh --o test.mgh fsaverage_sym lh white Number of vertices 163842 Number of faces327680 Total area 61972.710938 GroupSurface 85910.812500 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh... Loading mask mask.mgh Found 158531 voxels in mask Polynomial detrending, order = 0 Smoothing input by fwhm=4.00, gstd=1.698644, niters=11 Computing spatial AR1 ar1mn = 0, ar1std = 0, ar1max = 0 avg vertex dist 0.693419 WARNING: ar1 = 0 = 0. Setting fwhm to 0. avg vertex dist 0.693419 fwhm = 0.00 ___ 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.
Re: [Freesurfer] warning after running mris_fwhm
Thanks Doug. Yes, it works well now! -Glen On Thu, May 23, 2013 at 1:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The second error just means that it cannot compute the fwhm. This will go away if you add --smoooth-only. On 05/23/2013 01:31 PM, Glen Lee wrote: Hello FreeSurfer experts, I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices. Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 =0) may be critical. If anyone has any idea/ suggestions, please help. -Glen mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4 --i rabold4_0065_sym_L.mgh --o test.mgh fsaverage_sym lh white Number of vertices 163842 Number of faces327680 Total area 61972.710938 GroupSurface 85910.812500 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh... Loading mask mask.mgh Found 158531 voxels in mask Polynomial detrending, order = 0 Smoothing input by fwhm=4.00, gstd=1.698644, niters=11 Computing spatial AR1 ar1mn = 0, ar1std = 0, ar1max = 0 avg vertex dist 0.693419 WARNING: ar1 = 0 = 0. Setting fwhm to 0. avg vertex dist 0.693419 fwhm = 0.00 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer 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] Why does smoothing make non-zero intensity to zero in many vertices?
Thanks Doug. I'll give it a try right away. Glen On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug ps. Please remember to send to the list and not to me directly. That way others can benefit from the exchange and the record goes into our mail archive. On 05/09/2013 11:07 AM, Glen Lee wrote: Hi Doug See below for the command line that I used. smoothK=4; mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ... num2str(smoothK) ' --cortex --sval ' Functional_dir Subj '/GLM/all_base-sym_R.mgh '... On Wed, May 8, 2013 at 11:31 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Hi Glen, can you give us more information about what you did? Eg, command line? doug On 5/8/13 8:53 PM, Glen Lee wrote: Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2surf (with fwhm ==4) and examined the values in the output map. As it turns out, values become 0 in a number of vertices after smoothing while those in many other vertices look normal (i.e., more or less similar to the values in the vertex of unsmoothed map). I'm not sure why this happened as smoothing average values locally within the kernel (4mm). Any helpful answers would be greatly appreciated. Glen p.s) fyi, the original EPI is a slap data covering only the temporal occipital cortex. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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] Why does smoothing make non-zero intensity to zero in many vertices?
You are right, Doug. The number of zero-value vertices got reduced more and more when I increased the smoothing kernel size. Thanks a lot for your help! -Glen On Thu, May 9, 2013 at 3:29 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: command looks ok. Just using a slab would create 0s in a lot of places, but those 0s should get smoothed with other non 0s On 05/09/2013 02:06 PM, Glen Lee wrote: On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug - there was some improvement when I did smoothing after removed '-- cortex flag', such that the number of vertex with '0' was decreased from 35785 to 21898. I piped in a slab EPI image (covering only temporal regions) to the freesurfer using mri_vol2surf function (see below for more details). I'm guessing this has caused some holes (i.e., zero-value vertices) in labels during 2D reconstruction? Or alternatively, do you see any problem in the command below? mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' num2str(run) zero_digit num2str(TR) '.nii' ... ' --srcreg ~/DMPC/3D/data/' Subj '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR) '_R.mgh']; -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?
Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2surf (with fwhm ==4) and examined the values in the output map. As it turns out, values become 0 in a number of vertices after smoothing while those in many other vertices look normal (i.e., more or less similar to the values in the vertex of unsmoothed map). I'm not sure why this happened as smoothing average values locally within the kernel (4mm). Any helpful answers would be greatly appreciated. Glen p.s) fyi, the original EPI is a slap data covering only the temporal occipital cortex. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to flip L/R image in the freeview?
Freesurfer users, I'm a newbie for FS and have a rudimentary question for you. I have to overlay the group map for right hemisphere onto the lh.inflated (due to using sym space, where left surface map became symmetrical to the right), but I wonder if there is any way of reverting it back to rh.inflated after the overlay using the freeview software. Your help would be appreciated. -Glen ___ 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 warning: invalid drawable
Dear freesurfer experts, I'm wondering why I get this warning message when I open up any surf template in either fsaverage or fsaverage_sym directory. FYI, I'm using freeview v1.0 if anybody know, please help. -Glen $ freeview -f lh.inflated 2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) 2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable ___ 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] the mid point slide bar doesn't come back to 0 by manually entering 0 in the freeview
Hi freesurfer experts, I'm a newbie for the free surfer and am playing around with the freeview GUI. I'm having trouble moving the slide bar back to '0' by manually entering '0' right next to the Mid point slide. Interestingly, the slide bar moves when I entered other values like -2 or 2, but it doesn't when I entered 0. I wonder if it happens to my computer or a minor bug in the GUI. Glen ___ 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] [freesurfer] a puzzling installation error
Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory although I've downloaded the file and move that to the usr/local directory, so there clearly is the file. Would anybody help me how to resolve this issue? Below is the error message and platform info. Many thanks! -GL --- g...@ubuntu:/usr/local$ uname -a Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC 2010 i686 GNU/Linux. tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/surf/ tar: freesurfer/average/surf: Cannot mkdir: No such file or directory freesurfer/average/surf/lh.sphere.reg tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or directory freesurfer/average/surf/rh.sphere.reg tar: freesurfer/average/surf/rh.sphere.reg: C ___ 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] [freesurfer] installation failure
Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory when I simply followed the instruction by typing the command below in the /usr/local directory. tar xzvf freesurfer-Linux-centos4-stable-pub-v4.5.0-full.tar.gz Would anybody help me how to resolve this issue? Below is the error message and platform info. Many thanks! -GL --- g...@ubuntu:/usr/local$ uname -a Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC 2010 i686 GNU/Linux. tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/surf/ tar: freesurfer/average/surf: Cannot mkdir: No such file or directory freesurfer/average/surf/lh.sphere.reg tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or directory freesurfer/average/surf/rh.sphere.reg tar: freesurfer/average/surf/rh.sphere.reg: Cannot open: No such file or directory freesurfer/average/lh.atlas2002_simple.gcs tar: freesurfer/average/lh.atlas2002_simple.gcs: Cannot open: No such file or directory freesurfer/average/rigidly_aligned_brain_template.tif tar: freesurfer/average/rigidly_aligned_brain_template.tif: Cannot open: No such file or directory freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr: Cannot open: No such file or directory freesurfer/average/mni305.cor.subfov1.reg tar: freesurfer/average/mni305.cor.subfov1.reg: Cannot open: No such file or directory freesurfer/average/rh.average.CURVATURE.tif tar: freesurfer/average/rh.average.CURVATURE.tif: Cannot open: No such file or directory freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs tar: freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs: Cannot open: No such file or directory freesurfer/average/mni_average_305.4dfp.img.rec tar: freesurfer/average/mni_average_305.4dfp.img.rec: Cannot open: No such file or directory freesurfer/average/rh.average.curvature.filled.buckner40.tif tar: freesurfer/average/rh.average.curvature.filled.buckner40.tif: Cannot open: No such file or directory freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.mat tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.mat: Cannot open: No such file or directory freesurfer/average/mni_average_305.4dfp.ifh tar: freesurfer/average/mni_average_305.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/mni305.cor.subfov2.reg tar: freesurfer/average/mni305.cor.subfov2.reg: Cannot open: No such file or directory freesurfer/average/mni_average_305.4dfp.img tar: freesurfer/average/mni_average_305.4dfp.img: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh: Cannot open: No such file or directory freesurfer/average/face.gca tar: freesurfer/average/face.gca: Cannot open: No such file or directory freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs tar: freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec: Cannot open: No such file or directory freesurfer/average/rh.average.tif tar: freesurfer/average/rh.average.tif: Cannot open: No such file or directory freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs tar: freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs: Cannot open: No such file or directory freesurfer/average/711-2C_as_mni_average_305.4dfp.img tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img: Cannot open: No such file or directory freesurfer/average/mni152.register.dat tar: freesurfer/average/mni152.register.dat: Cannot open: No such file or directory freesurfer/average/RB_all_2007-08-08.gca tar: freesurfer/average/RB_all_2007-08-08.gca: Cannot open: No such file or directory freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img tar: freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img: Cannot open: No such file or directory freesurfer/average/mni305.cor.readme tar: freesurfer/average/mni305.cor.readme: Cannot open: No such file or directory
[Freesurfer] Which version should I download?
Hello, I just installed a recent version of Ubuntu to run the freesurfer and I know nothing about Linux yet. But I'm seeing that the download link only specifies CenOS 4. Does it mean that Ubuntu is not compatible with Freesurfer? Any help would be appreciated. Thanks, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
