Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] Mris_anatomical_stats problem
by Douglas N Greve 24 May '11

24 May '11

Jurgen, Both of these files were created with identical command lines. doug Jürgen Hänggi wrote: > Hi Doug > > Attached are the two files generated from the same subject by using > mris_anatomical_stats, once without smoothing (rh.aparc.a2005s.stats) and > once with smoothing (rh.aparc.a2005s_with_smoothing.stats). > > But the same results appear. This is also the case if I first use > mri_smooth2smooth to smooth the area map first. > > I recognised that the volume or thickness information changed with > smoothing, but the area information remained the same for smoothed and > unsmoothed data. > > Thans > Jürgen > > > On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: > > >> Can you send me the output stats file for both? >> >> Jürgen Hänggi wrote: >> >>> Hi Doug >>> >>> Yes, exactly that was the problem >>> >>> Thanks >>> Cheers >>> Jürgen >>> >>> >>> >>> >>> On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: >>> >>> >>> >>>> Hi Jurgen, did you say that the results with the smoothing and without >>>> the smoothing are identical? Is that what the problem is? >>>> >>>> doug >>>> >>>> Jürgen Hänggi wrote: >>>> >>>> >>>>> Hi Doug >>>>> >>>>> Here is the output from the terminal when running mris_anatomical_stats. I >>>>> have run a loop, but show only the output of one subject. The smoothed file >>>>> is rg.area_smooth.mgh and the output file is called like the old aparc file >>>>> in order to be readable with aparcstats2table. >>>>> >>>>> foreach s ( biid_* ) >>>>> foreach? mris_anatomical_stats -a area_p01.annot -t rh.area_smooth.mgh -f >>>>> $s/stats/rh.aparc.a2005s.stats $s rh >>>>> foreach? end >>>>> computing statistics for each annotation in area_p01.annot. >>>>> using thickness file rh.area_smooth.mgh. >>>>> reading volume /Applications/freesurfer/subjects/biid_b101/mri/wm.mgz... >>>>> reading input surface >>>>> /Applications/freesurfer/subjects/biid_b101/surf/rh.white... >>>>> reading input pial surface >>>>> /Applications/freesurfer/subjects/biid_b101/surf/rh.pial... >>>>> reading input white surface >>>>> /Applications/freesurfer/subjects/biid_b101/surf/rh.white... >>>>> reading colortable from annotation file... >>>>> colortable with 14 entries read (originally none) >>>>> structure is "cluster-001" >>>>> number of vertices = 138 >>>>> total surface area = 88 mm^2 >>>>> total gray matter volume = 62 mm^3 >>>>> average cortical thickness = 0.663 mm +- 0.048 mm >>>>> average integrated rectified mean curvature = 0.188 >>>>> average integrated rectified Gaussian curvature = 0.065 >>>>> folding index = 5 >>>>> intrinsic curvature index = 0.4 >>>>> structure is "cluster-002" >>>>> number of vertices = 111 >>>>> total surface area = 84 mm^2 >>>>> total gray matter volume = 42 mm^3 >>>>> average cortical thickness = 0.751 mm +- 0.033 mm >>>>> average integrated rectified mean curvature = 0.129 >>>>> average integrated rectified Gaussian curvature = 0.020 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-003" >>>>> number of vertices = 122 >>>>> total surface area = 75 mm^2 >>>>> total gray matter volume = 44 mm^3 >>>>> average cortical thickness = 0.671 mm +- 0.027 mm >>>>> average integrated rectified mean curvature = 0.098 >>>>> average integrated rectified Gaussian curvature = 0.021 >>>>> folding index = 0 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-004" >>>>> number of vertices = 415 >>>>> total surface area = 269 mm^2 >>>>> total gray matter volume = 178 mm^3 >>>>> average cortical thickness = 0.690 mm +- 0.034 mm >>>>> average integrated rectified mean curvature = 0.132 >>>>> average integrated rectified Gaussian curvature = 0.033 >>>>> folding index = 4 >>>>> intrinsic curvature index = 0.6 >>>>> structure is "cluster-005" >>>>> number of vertices = 131 >>>>> total surface area = 76 mm^2 >>>>> total gray matter volume = 66 mm^3 >>>>> average cortical thickness = 0.671 mm +- 0.055 mm >>>>> average integrated rectified mean curvature = 0.106 >>>>> average integrated rectified Gaussian curvature = 0.031 >>>>> folding index = 2 >>>>> intrinsic curvature index = 0.2 >>>>> structure is "cluster-006" >>>>> number of vertices = 223 >>>>> total surface area = 145 mm^2 >>>>> total gray matter volume = 139 mm^3 >>>>> average cortical thickness = 0.665 mm +- 0.185 mm >>>>> average integrated rectified mean curvature = 0.146 >>>>> average integrated rectified Gaussian curvature = 0.073 >>>>> folding index = 3 >>>>> intrinsic curvature index = 0.6 >>>>> structure is "cluster-007" >>>>> number of vertices = 45 >>>>> total surface area = 37 mm^2 >>>>> total gray matter volume = 36 mm^3 >>>>> average cortical thickness = 0.780 mm +- 0.060 mm >>>>> average integrated rectified mean curvature = 0.138 >>>>> average integrated rectified Gaussian curvature = 0.048 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.0 >>>>> structure is "cluster-008" >>>>> number of vertices = 150 >>>>> total surface area = 81 mm^2 >>>>> total gray matter volume = 53 mm^3 >>>>> average cortical thickness = 0.578 mm +- 0.067 mm >>>>> average integrated rectified mean curvature = 0.142 >>>>> average integrated rectified Gaussian curvature = 0.081 >>>>> folding index = 10 >>>>> intrinsic curvature index = 0.8 >>>>> structure is "cluster-009" >>>>> number of vertices = 74 >>>>> total surface area = 51 mm^2 >>>>> total gray matter volume = 36 mm^3 >>>>> average cortical thickness = 0.719 mm +- 0.042 mm >>>>> average integrated rectified mean curvature = 0.169 >>>>> average integrated rectified Gaussian curvature = 0.052 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-010" >>>>> number of vertices = 55 >>>>> total surface area = 31 mm^2 >>>>> total gray matter volume = 26 mm^3 >>>>> average cortical thickness = 0.631 mm +- 0.037 mm >>>>> average integrated rectified mean curvature = 0.153 >>>>> average integrated rectified Gaussian curvature = 0.090 >>>>> folding index = 2 >>>>> intrinsic curvature index = 0.2 >>>>> structure is "cluster-011" >>>>> number of vertices = 78 >>>>> total surface area = 45 mm^2 >>>>> total gray matter volume = 21 mm^3 >>>>> average cortical thickness = 0.662 mm +- 0.036 mm >>>>> average integrated rectified mean curvature = 0.113 >>>>> average integrated rectified Gaussian curvature = 0.017 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-012" >>>>> number of vertices = 4 >>>>> total surface area = 4 mm^2 >>>>> total gray matter volume = 4 mm^3 >>>>> average cortical thickness = 0.824 mm +- 0.010 mm >>>>> average integrated rectified mean curvature = 0.052 >>>>> average integrated rectified Gaussian curvature = 0.003 >>>>> folding index = 0 >>>>> intrinsic curvature index = 0.0 >>>>> structure is "cluster13" >>>>> number of vertices = 8 >>>>> total surface area = 4 mm^2 >>>>> total gray matter volume = 3 mm^3 >>>>> average cortical thickness = 0.634 mm +- 0.021 mm >>>>> average integrated rectified mean curvature = 0.133 >>>>> average integrated rectified Gaussian curvature = 0.026 >>>>> folding index = 0 >>>>> intrinsic curvature index = 0.0 >>>>> computing statistics for each annotation in area_p01.annot. >>>>> using thickness file rh.area_smooth.mgh. >>>>> >>>>> Thanks >>>>> Cheers >>>>> Jürgen >>>>> >>>>> On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Juegen, can you send the full terminal output? Also, you can try >>>>>> explicitly smoothing the file with mri_surf2surf and then run anatomical >>>>>> stats on the smoothed file. >>>>>> doug >>>>>> >>>>>> Jürgen Hänggi wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Dear FS experts >>>>>>> >>>>>>> I tried to read out in each subject the surface area values of some >>>>>>> clusters >>>>>>> derived from a group comparison. >>>>>>> For that purpose, I used mri_surf2surf and mris_anatomical_stats. >>>>>>> >>>>>>> Everything worked fine, but in some clusters the direction of the effects >>>>>>> reversed. A first guess was that this might have to do with the smoothing >>>>>>> that we applied to the group comparison. >>>>>>> >>>>>>> Therefore, I smoothed the individual area files to get the smoothed >>>>>>> surface >>>>>>> area in each subject using the following command: >>>>>>> >>>>>>> mris_anatomical_stats -a area_p01.annot -t rh.area -nsmooth 15 -f >>>>>>> $s/stats/rh.aparc.a2005s.stats $s rh >>>>>>> >>>>>>> But the surface area of this smoothed data gives the same values as the >>>>>>> unsmoothed data. >>>>>>> >>>>>>> Any idea what is wrong here? >>>>>>> >>>>>>> Thanks in advance >>>>>>> Regards >>>>>>> Jürgen >>>>>>> >>>>>>> PS: sorry for posting this message twice, but the first post did not >>>>>>> appeared in the archives >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>> --------------------------------------------------------------------------->> >>> >>> - >>> >>> >>>>>>> Jürgen Hänggi, Ph.D. >>>>>>> Division Neuropsychology >>>>>>> Institute of Psychology >>>>>>> University of Zurich >>>>>>> Binzmuehlestrasse 14, PO Box 25 >>>>>>> 8050 Zurich, Switzerland >>>>>>> 0041 44 635 73 97 (phone office) >>>>>>> 0041 76 445 86 84 (phone mobile) >>>>>>> 0041 44 635 74 09 (fax office) >>>>>>> BIN 4.D.04 (office room number) >>>>>>> j.haenggi[at]psychologie.uzh.ch (email) >>>>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>>>> http://www.juergenhaenggi.ch (private website) >>>>>>> >>>>>>> This e-mail (and any attachment/s) contains confidential and/or >>>>>>> privileged >>>>>>> information. If you are not the intended recipient (or have received this >>>>>>> e-mail in error) please notify the sender immediately and destroy this >>>>>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>>>>> material in this e-mail is strictly forbidden. >>>>>>> >>>>>>> >>>>>>> >>> --------------------------------------------------------------------------->> >>> >>> - >>> >>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> > --------------------------------------------------------------------------->>>> > - > >>>>> Jürgen Hänggi, Ph.D. >>>>> Division Neuropsychology >>>>> Institute of Psychology >>>>> University of Zurich >>>>> Binzmuehlestrasse 14, PO Box 25 >>>>> 8050 Zurich, Switzerland >>>>> 0041 44 635 73 97 (phone office) >>>>> 0041 76 445 86 84 (phone mobile) >>>>> 0041 44 635 74 09 (fax office) >>>>> BIN 4.D.04 (office room number) >>>>> j.haenggi[at]psychologie.uzh.ch (email) >>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>> http://www.juergenhaenggi.ch (private website) >>>>> >>>>> This e-mail (and any attachment/s) contains confidential and/or privileged >>>>> information. If you are not the intended recipient (or have received this >>>>> e-mail in error) please notify the sender immediately and destroy this >>>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>>> material in this e-mail is strictly forbidden. >>>>> >>>>> > --------------------------------------------------------------------------->>>> > - > >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> ---------------------------------------------------------------------------- >>> Jürgen Hänggi, Ph.D. >>> Division Neuropsychology >>> Institute of Psychology >>> University of Zurich >>> Binzmuehlestrasse 14, PO Box 25 >>> 8050 Zurich, Switzerland >>> 0041 44 635 73 97 (phone office) >>> 0041 76 445 86 84 (phone mobile) >>> 0041 44 635 74 09 (fax office) >>> BIN 4.D.04 (office room number) >>> j.haenggi[at]psychologie.uzh.ch (email) >>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>> http://www.juergenhaenggi.ch (private website) >>> >>> This e-mail (and any attachment/s) contains confidential and/or privileged >>> information. If you are not the intended recipient (or have received this >>> e-mail in error) please notify the sender immediately and destroy this >>> e-mail. Any unauthorised copying, disclosure or distribution of the >>> material in this e-mail is strictly forbidden. >>> ---------------------------------------------------------------------------- >>> >>> >>> >>> >>> >>> >>> > > > ---------------------------------------------------------------------------- > Jürgen Hänggi, Ph.D. > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > ---------------------------------------------------------------------------- > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

skull strip T2 image in Freesurfer
by Xiaoying Tang 24 May '11

24 May '11

Hi All, I am wondering whether there is any way to skull strip a T2 image using freesurfer. I tried to use the same way as for skullstripping T1 image, but always failed. I would be most grateful if someone can give me some suggestion. Best, Xiaoying Tang

4 13

Making a custom experimental template
by Joakim Vinberg 24 May '11

24 May '11

Hi FS crowd, I just want to make sure that I have the process correctly described for setting up a custom experimental template. I am basing this off of the SurfaceRegAndTemplates (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and a hypothetical experiment with 10 subjects (s1, s2, ...s10). I apologize if this has been well-covered-I couldn't quite match it on the website or the archives. For the prep step, I believe my commands would be: mris_make_template lh sphere s1 custom_template_lh_0.tif mris_make_template rh sphere s1 custom_template_rh_0.tif which would result in two new template files names custom_template_lh_0.tif and custom_template_rh_0.tif For Round 1, I would first create another registration for each subject: mris_register s1/surf/lh.sphere custom_template_lh_0.tif s1/surf/lh.sphere.regcustom_0 mris_register s1/surf/rh.sphere custom_template_rh_0.tif s1/surf/rh.sphere.regcustom_0 ... mris_register s10/surf/lh.sphere custom_template_lh_0.tif s10/surf/lh.sphere.regcustom_0 mris_register s10/surf/rh.sphere custom_template_rh_0.tif s10/surf/rh.sphere.regcustom_0 And then create another custom template: mris_make_template lh sphere s1 s2 s3 ... s10 custom_template_lh_1.tif mris_make_template rh sphere s1 s2 s3 ... s10 custom_template_rh_1.tif For round 2, I would repeat Round 1, generating a new set of sphere.reg files, and then a new template, except substitute the custom template from round 1 (custom_template_lh_1.tif and custom_template_rh_1.tif). Then, I would register all of my data to the custom_template_lh_2.tif and custom_template_rh_2.tif generated at the end of round 2. From there, I am assuming that I could be able to use this new template as I would fsaverage. Am I correct, or have I missed a step? Thanks in advance for all of your help! Joakim

4 7

Download source code from repository
by Jordi Delgado 24 May '11

24 May '11

Hi Freesurfers, I'm trying to download the FreeSurfer's source code from de repository using: cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev and I obtain this message: cvs checkout: authorization failed: server fsvm.nmr.mgh.harvard.edu rejected access to /usr/fscvsroot for user anonymous Is there any problem with the repository? Thank you in advance!

1 0

tksurfer' configure overlay window incomplete...
by Gonzalo Rojas Costa 23 May '11

23 May '11

Hi: I have an ubuntu based computer with Freesurfer 5.0.0, and the lowest part of the View->Configure->Overlay window of tksurfer didn't appears (see attached image)... How can I correct it ?... The PC has 1440x900 of screen resolution... How can I view the complete window ?... In another PC with 1920x1080 of screen resolution, Freesurfer 4.5.0 and another Ubuntu version, that tksurfer window looks ok (see atached image)... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

3 2

question abt fsaverage V1
by Ritobrato Datta 23 May '11

23 May '11

Hello All, I noticed that that there is a fsaverage/label/?h.V1.label Is this label created from the Hinds and Fischl method ? Can someone give some details abt it ? Also for individual subjects, when I run the V1 estimation using Hinds and Fischl method, how accurate are the V1 / V2 border compared to retinotopy ? Or which is more accurate ? Thanks Ri

3 2

Running FreeSurfer Remotely
by obregon＠nmr.mgh.harvard.edu 23 May '11

23 May '11

Hi, Will FreeSurfer run remotely using NX Client for OSX or should I employ VNC only? Thanks, Gabriel

3 2

loading qdec.table.dat error
by Tetiana Dadakova 23 May '11

23 May '11

Dear list, I am trying to load qdec.table.dat file using qdec, and get the following error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 126 ERROR: QdecDataTable::Load: problem parsing file /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat This line did not appear to end with a newline: PAT_ViOl 25 pat Error loading the data table. This is the last line in the file and therefore there is no new line after it. What can cause this error? Thank you, Tanja.

2 3

flattenning question
by Gabriel Go.Es. 20 May '11

20 May '11

Dear FreeSurfers I'm wondering about the flattenning options of FS I've saw that the "mris-flatten" command does the trick but, it asks for a patch, my questions are: can I flat any cortical region? and, how do I create a patch to mris_flatten? Thanks in advanced, Gabriel

3 5

FW: What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?
by Righart, Ruthger Dr. 20 May '11

20 May '11

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 [astevens(a)nmr.mgh.harvard.edu] Sent: Friday, May 20, 2011 2:56 PM To: Righart, Ruthger Dr. Cc: freesurfer(a)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.Righart(a)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.Righart(a)med.uni-muenchen.de > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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.

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer