[Freesurfer] longitudinal TRACULA
Hi, I've run cross-sectional TRACULA on one subject, three different timepoints. Now I'm trying to run a longitudinal analysis on the same subject's 3 timepoints. My understanding was that for TRACULA, unlike for morphometry, I don't need to first run cross sectional before longitudinal, the only requirement is that I have a longitudinal dmrirc file that specifies the timepoints with their corresponding files. It crashed with these error messages: #@# Inter-subject registration (base template) lø. 29. juli 14:25:45 +0200 2017 cp /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_base/dmri/xfms cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat': No such file or directory Linux compute-16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any idea what went wrong here? Thank you! Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's University Hospital 7006 Trondheim Norway ___ 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] problem with bedpostx
Hi,
Running trac-all -bedp and getting an error message I've never seen before.
I'm running it on a desktop, not a cluster, which it warns agains - but it
should still run, shouldn't it?
larsrim:~/lbkabel/tbi/morfometri_test$ trac-all -bedp -c
DWI/jobscripts/d1_1001_local.dmrirc
INFO: SUBJECTS_DIR is /home/larsrim/lbkabel/tbi/morfometri_test
INFO: Diffusion root is
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2
/home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
Sincerely yours,
Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Functional MRI
Department of Radiology
St. Olav's University Hospital
7006 Trondheim
Norway
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[Freesurfer] problems with recon-all in 6.0
Hi, I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting error messages and some strange behavior: ls 01001/0/2/ 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm 4.dcm 55.dcm 60.dcm 66.dcm 71.dcm 77.dcm 82.dcm 88.dcm 93.dcm 99.dcm 101.dcm 107.dcm 112.dcm 118.dcm 123.dcm 129.dcm 134.dcm 13.dcm 145.dcm 150.dcm 156.dcm 161.dcm 167.dcm 172.dcm 18.dcm 23.dcm 29.dcm 34.dcm 3.dcm 45.dcm 50.dcm 56.dcm 61.dcm 67.dcm 72.dcm 78.dcm 83.dcm 89.dcm 94.dcm 9.dcm 102.dcm 108.dcm 113.dcm 119.dcm 124.dcm 12.dcm 135.dcm 140.dcm 146.dcm 151.dcm 157.dcm 162.dcm 168.dcm 173.dcm 19.dcm 24.dcm 2.dcm 35.dcm 40.dcm 46.dcm 51.dcm 57.dcm 62.dcm 68.dcm 73.dcm 79.dcm 84.dcm 8.dcm 95.dcm 103.dcm 109.dcm 114.dcm 11.dcm 125.dcm 130.dcm 136.dcm 141.dcm 147.dcm 152.dcm 158.dcm 163.dcm 169.dcm 174.dcm 1.dcm 25.dcm 30.dcm 36.dcm 41.dcm 47.dcm 52.dcm 58.dcm 63.dcm 69.dcm 74.dcm 7.dcm 85.dcm 90.dcm 96.dcm 104.dcm 10.dcm 115.dcm 120.dcm 126.dcm 131.dcm 137.dcm 142.dcm 148.dcm 153.dcm 159.dcm 164.dcm 16.dcm 175.dcm 20.dcm 26.dcm 31.dcm 37.dcm 42.dcm 48.dcm 53.dcm 59.dcm 64.dcm 6.dcm 75.dcm 80.dcm 86.dcm 91.dcm 97.dcm 105.dcm 110.dcm 116.dcm 121.dcm 127.dcm 132.dcm 138.dcm 143.dcm 149.dcm 154.dcm 15.dcm 165.dcm 170.dcm 176.dcm 21.dcm 27.dcm 32.dcm 38.dcm 43.dcm 49.dcm 54.dcm 5.dcm 65.dcm 70.dcm 76.dcm 81.dcm 87.dcm 92.dcm 98.dcm recon-all -subject 1001_c1 -i 01001/0/2/1.dcm -all writing to /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig/001.mgz... # #@# MotionCor fr. 14. juli 10:04:21 +0200 2017 ERROR: no run data found in /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri. Make sure to have a volume called 001.mgz in /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux compute-16-36.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s �1001_c1 exited with ERRORS at fr. 14. juli 10:04:21 +0200 2017 Not sure why it crashes, and why does it add "?" to the subject name? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] tracula reinit
Hi Anastasia! That makes sense, thank you! So the question is how do I evaluate the noisiness of a path? 1) Most of my isosurfaces look a lot noisier than your example on the wiki. There's obviously no hard and fast rule here but is there any way to gauge the noisiness of a reconstructed path? And can that information be used for quality control? 2) Another source of information on outliers is the log files that are produced when running -trac-all -stat (based on the shape of the tract). It doesn't seem to flag tracts that are (almost) completely missing (which are spotted by visual inspection in Freeview) - but they may fall under the minimum threshold and therefore not be evaluated? Would you recommend automatically excluding the subjects that are flagged as outliers here? >Hi Lars - A path with fewer control points will generally be smoother. So >if the tract is pretty much a straight line, you might get a noisier >result if you increase the number of control points. But if the tract is >more convoluted than a straight line, then you need more control points to >define it accurately. So it's hard to predict the result of increasing the >control points in general, it depends on the specific case. >BTW, if you change the number of control points, you don't need to use the >reinit variable - that's only for rerunning with the same control points >as before. > >Best, >a.y sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] tracula reinit
Hi, Rerunning the tractography using reinit, is it an absolute requirement to specify number of control points? It doesn't seem like I can just set reinit = 1 and let the number of control points be the default. Also, is there a trade-off in terms of number of control points? For instance, when reconstructing the forceps major, the default number of control points is already 7, i.e. the highest of any tract. What if I double it? Apart from the fact that it takes longer, is there any drawback to using lots of controls points? Thank you! LMR ___ 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] trac-all -path Segmentation fault
Hi, I ran trac-all -prep and bedpostx successfully and qc (in accordance with tutorial) was fine but trac-all -path failed, due to "Segmentation fault" on two subjects: Segmentation fault Linux compute-16-6.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at ti. 20. sep. 09:40:55 +0200 2016 - Segmentation fault Linux compute-16-14.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at ti. 20. sep. 09:30:07 +0200 2016 Where do I go next? sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] trac-all error (bvecs and bvals don't have same number of entries)
Hi Anastasia,
I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").
thank you!
LMR
Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and
dmri/bvecs files that get generated look fine too?
a.y
On Sat, 2 Jul 2016, Lars M. Rimol wrote:
Hi,
Trying to run trac-all -c dmric_file -prep, I get an error message stating
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).
OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated
Tracula and FSL (v 5.0.9).
Error message:
#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
-r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC
2015 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016
--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?
I have attached the bval/bvec files and the trac-all.log.
---
The contents of the dmric file is:
setenv SUBJECTS_DIR /media/lmr2/subjects/DTI
set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot = /media/lmr2/subjects/DTI
set dcmlist = ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv
Thank you!
yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
bvals_rows
Description: Binary data
bvec_rows
Description: Binary data
bvals
Description: Binary data
bvecs
Description: Binary data
dwi_orig.mghdti.bvals
Description: Binary data
dwi_orig.mghdti.bvecs
Description: Binary data
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[Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)
Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 -- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. --- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway 0100010001000100010001000100010001000100010001000100010001000100010001000100010001000100010001000100010001000100010001000200020002000200020002000200020002000200020002000200020002000200020002000200020002000200020002000200020002000200020002000000 0-0.203770.197880.40243-0.40388-0.20233-0.85342-0.73137-0.40767-0.73256-0.65079-0.32244-0.32447-0.65033-0.97858-0.854560.000732920.00315550.654590.329460.198010.204310.651670.324360.200460.403880.732220.728930.852650.857480.97941-0.203830.198380.40215-0.40386-0.20227-0.85391-0.73143-0.40738-0.73222-0.65118-0.32277-0.32447-0.65021-0.97877-0.854070.00107460.00268950.654090.329750.198530.203820.651980.32440.200420.403860.731880.72890.853130.857030.97941000 00.518990.519780.175390.730860.941570.517940.519370.175710.175450.729840.940860.518740.519450.176170.175370.730840.941440.518290.51954-0.176060.175980.729740.940790.940340.730860.175540.518330.518510.175730.175210.517810.518440.174530.729920.94110.516920.518140.174850.174420.729130.940570.517830.518150.174740.174620.729960.941040.517570.51819-0.174480.174570.729150.940640.940040.729920.174430.517530.517490.174570.17459000 00.830130.831060.898490.55020.269290.0584620.441990.896060.6577-0.20929-0.104-0.79096-0.55429-0.10651-0.48884-0.68255-0.33718-0.55035-0.788370.96426-0.96296-0.20688-0.0985390.274910.55020.658060.447210.064332-0.48358-0.10030.830860.831780.898780.551460.270960.0602960.443330.896360.65836-0.21059-0.10562-0.79157-0.55565-0.10708-0.48997-0.68349-0.33829-0.55161-0.789140.96444-0.96332-0.20797-0.0998280.275970.551460.658720.448190.066168-0.48479-0.10137000 bvals Description: Binary data bvec Description: Binary data lø. 02. juli 09:47:59 +0200 2016 /media/lmr2/subjects/DTI /usr/local/freesurfer/bin/trac-all -c dmric_test_mars2015 -prep Subject 4_FS SUBJECTS_DIR /media/lmr2/subjects/DTI FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 lmr dmed4870 Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC
[Freesurfer] visualizing statistical maps in FreeView
Hi, Is it possible to overlay .mgh files with statistics (e.g. p-maps) directly in FreeView, for purposes of visualizing the results, the same way you can in tksurfer? When I try load an overlay in FreeView, it seems to be expecting a volume file. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] FLIRT in Han et al., 2006
Hi, I wish to test the reliability of series of three T1 scans that were collected over a period of a few months. The Han et al., 2006 paper recommends using FLIRT to do a linear registration between the scans and then the volumetric registration matrix is applied to the corresponding surfaces (please see quote at the bottom of this e-mail). I was wondering if this is the way to reproduce what was done in that paper: 1) recon-all -all on all three scans 2) register e.g., the 001.mgz from tp2 and tp3 to tp1 using FLIRT; which timepoint was chosen as the reference tp in Han et al.? Or was some type of average template created? Registering all other images to one timepoint seems contrary to the thinking behind the FreeSurfer longitudinal stream (which of course didn't exist at that time). Would you recommend using the FS longitudinal stream in stead? 3) apply the registration matrix to 'h.area and *h.thickness. Here the question is how do I apply the registration matrix to the area and thickness files? I saw mris_apply_reg was recommended in order to register to xhemi.rh.w-g.pct.mgh but I'm not sure if I can use mris_apply_reg here? from the 2006 paper: "[..] a simpler linear registration is adopted to perform the intrasubject surface alignment, and surface point correspondence is then built according to their Euclidean distance in the registered space [..]. The linear registration is computed using the FLIRT linear registration tool (Jenkinson et al., 2002). The volumetric registration matrix is then applied to the corresponding surfaces." Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] asegstats2table list index out of range
Hi, I'm trying to run asegstats2table asegstats2table --subjects subjlist.csv --skip --delimiter comma --common-segs --tablefile asegs_03042016.csv All subjects in the subjlist are present in the directory but I get this error message: Parsing the .stats files Building the table.. Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 560, in rows, columns, table = sanitize_table(options, pretable) File "/usr/local/freesurfer/bin/asegstats2table", line 454, in sanitize_table _specs, _id_name_map, _measl = _t[0] IndexError: list index out of range I get the error message even if I reduce the list to two subjects. It works if I do this (all subjdirs begin with PD): asegstats2table --subjects PD* --skip --delimiter comma --common-segs --tablefile asegs_03042016.csv And it works if I enter the subjects' names individually. With over 100 subjects, however, that's not an option. I'd be grateful for any suggestion on how to run asegstats2table with a subjects list. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] errors message in QAtools
Hi, I'm running QAtools on a set of subjects processed with FS 5.3.0, and consistently get this message when recon_checker is running: Processing each subcortical label ... (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error etc. *And in the recon_check file I notice several of my subjects have this error message:* ERROR: Recon-all steps missing in subject status file Expected to see the following step(s): #@# Remove Neck ti. 22. mars 15:02:33 +0100 2016 in the recon-all-status.log file before (line # 12): --> CA Reg Inv *I ran recon-all -all, and the recon-all log file seems to indicate neck removal was peformed*; from recon-all.log: mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... -- writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 51 seconds. #-- #@# SkullLTA ti. 22. mars 14:45:17 +0100 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta === NUMBER OF OPENMP THREADS = 1 === aligning to atlas containing skull, setting unknown_nbr_spacing = 5 -- reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) spacing=8, using 3481 sample points, tol=1.00e-05... Apart from this, the snapshots look ok (except for one subject I asked about in a previous e-mail) and there are no outliers in any of the subjects (according to QAtools). Any idea why I get this error message? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital 7006 Trondheim, Norway ___ 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] if: Expression Syntax.
Hi, I have a large amount of data (FS scanworkups) where all the files within every subject's directory are zipped. Is there a way to run mris_preproc on zipped data? For instance, mris_preproc crashes because it can't find lh.thickness unless I unzip it Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] mris_preproc on zipped data
Hi, I have a large amount of data (FS scanworkups) where all the files within every subject's directory are zipped. Is there a way to run mris_preproc on zipped data? For instance, mris_preproc crashes because it can't find lh.thickness unless I unzip it Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ 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] failure to start tksurfer
Hi, I'm unable to initiate tksurfer. Can anyone tell me why this happens? [10:57 lmr@dmed4870 lmr] > tksurfer fsaverage lh inflated subject is fsaverage hemiis lh surface is inflated surfer: current subjects dir: /home/lmr/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/lmr checking for nofix files in 'inflated' Reading image info (/home/lmr/subjects/fsaverage) Reading /home/lmr/subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /home/lmr/subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, trying double buffered window Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, no suitable display found sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Error in load_mgh
Hi,
I have downloaded freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and
running MATLAB R2015b I get an error message when trying to use load_mgh.
Any tips?
>> [test, M, mr_parms, volsz] = load_mgh('/.mgh');
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158)
switch type
(PS! I've tried chancing the file name to just lh.mgh but get the same
error message. And the file(s) exist and the path is correct.)
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
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[Freesurfer] configure overlay display in tksurfer by keyboard inputs
Hi all, I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am unable to set threshold values in the edit boxes in the configure overlay display in tksurfer. Does anybody know how to fix this (without specifying the threshold on the command line each time)? Thank you! yours, Lars M. Rimol, PhD Department of Medicine John A. Burns School of Medicine University of Hawai'i 1356 Lusitana Street, University Tower Honolulu, HI 96813 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all
Hi all, When trying to run recon-all longitudinal processing (*recon-all -base 060027 -tp 060027_S01 -all* ) on a single time point, we run into a problem at mri_robust_template, where it stops, doesn't really produce any specific error message but prints some help page of some kind. And then: recon-all -s subject1 exited with ERRORS at Wed Jul 22 18:05:55 etc. This is the last output from recon-all: mri_robust_template --mov /mnt/fs5/fs510/060027_S01/mri/norm.mgz --lta /mnt/fs5/fs510/060027/mri/transforms/060027_S01_to_060027.lta --template /mnt/fs5/fs510/060027/mri/norm_template.mgz --average 1 --sat 4.685 We have already run the cross-sectional processing on this subject, so all of those files are there. norm.mgz exists, but none the files mentioned after --lta and --template do not exist. But at least norm_template.mgz is the output of mri_robust_template, right? I'm unsure if 060027_S01_to_060027.lta is supposed to be there before mri_robust_template starts? Is that the problem or is it something else? Any help would be appreciated, Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] Tracula reinit
Hi, The various tracts have different default numbers of control points, with a higher number for more curved paths. In a previous mail Dr. Yendiki recommended changing the number of control points if several attempts rerunning reinit don't produce a satisfactory result. Is it always better to have a larger number of control points, except for the increase (I assume) in processing time? Or will a larger number produce a worse result for less curved tracts? yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error message recon-all
Hi, I keep getting this error message when running, or trying to run, recon-all. I suspect there is a file somewhere indicating that this subject has been run before. But all that is in the directory 3002 is dicom images. What is wrong? [LMR in subjects/DTI ] recon-all -subjid 3002 -i 3002/1.dcm ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. [LMR in subjects/DTI ] recon-all -subjid 3002 ERROR: nothing to do [LMR in subjects/DTI ] ls 3002 100.dcm 107.dcm 113.dcm 11.dcm 126.dcm 132.dcm 139.dcm 145.dcm 151.dcm 158.dcm 19.dcm 25.dcm 31.dcm 38.dcm 44.dcm 50.dcm 57.dcm 63.dcm 6.dcm 76.dcm 82.dcm 89.dcm 95.dcm 101.dcm 108.dcm 114.dcm 120.dcm 127.dcm 133.dcm 13.dcm 146.dcm 152.dcm 159.dcm 1.dcm 26.dcm 32.dcm 39.dcm 45.dcm 51.dcm 58.dcm 64.dcm 70.dcm 77.dcm 83.dcm 8.dcm 96.dcm 102.dcm 109.dcm 115.dcm 121.dcm 128.dcm 134.dcm 140.dcm 147.dcm 153.dcm 15.dcm 20.dcm 27.dcm 33.dcm 3.dcm 46.dcm 52.dcm 59.dcm 65.dcm 71.dcm 78.dcm 84.dcm 90.dcm 97.dcm 103.dcm 10.dcm 116.dcm 122.dcm 129.dcm 135.dcm 141.dcm 148.dcm 154.dcm 160.dcm 21.dcm 28.dcm 34.dcm 40.dcm 47.dcm 53.dcm 5.dcm 66.dcm 72.dcm 79.dcm 85.dcm 91.dcm 98.dcm 104.dcm 110.dcm 117.dcm 123.dcm 12.dcm 136.dcm 142.dcm 149.dcm 155.dcm 16.dcm 22.dcm 29.dcm 35.dcm 41.dcm 48.dcm 54.dcm 60.dcm 67.dcm 73.dcm 7.dcm 86.dcm 92.dcm 99.dcm 105.dcm 111.dcm 118.dcm 124.dcm 130.dcm 137.dcm 143.dcm 14.dcm 156.dcm 17.dcm 23.dcm 2.dcm 36.dcm 42.dcm 49.dcm 55.dcm 61.dcm 68.dcm 74.dcm 80.dcm 87.dcm 93.dcm 9.dcm 106.dcm 112.dcm 119.dcm 125.dcm 131.dcm 138.dcm 144.dcm 150.dcm 157.dcm 18.dcm 24.dcm 30.dcm 37.dcm 43.dcm 4.dcm 56.dcm 62.dcm 69.dcm 75.dcm 81.dcm 88.dcm 94.dcm yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] Fwd: comparing lme models
Hi Jorge, My original model is: Intercept + centered age + group + centered age x group + sex; and since I have only two time points I can have only one random factor (as you've stated previously). I have used intercept as the random factor. So, based on your reply, I should fit this model for the covariance: Intercept + centered age + centered age^2 + group + centered age x group + centered age^2 x group + sex; together with three different models for the mean, i.e. intercept, centered age and centered age2 as random factors. When you say different models for the mean, you mean different random factors, right? So I should compare these three random factors with the chi square test to see which random factor to use (i.e., which model for the mean). And then I can test for the significance of centered age, centered age^2, and the two interaction terms to see which fixed factors I can drop from the covariance model? Have I understood you correctly? Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Wed, Dec 17, 2014 at 5:00 PM, jorge luis jbernal0...@yahoo.es wrote: Hi Lars I'm not sure whether you are talking about comparing different statistical models with the same model for the mean but different models for the covariance or comparing models with different models for the mean itself. In order to use the lreml/chi square test for model comparison you need to have the same model for the mean. In your case it should include: intercept + age + age^2 Then you select which of these variables are going to be treated as random effects based on the appropriate lreml/chi square test. After you select the random effects then you can perform statistical inferences (F-test) to determine whether your age^2 term is significant. If not significant you can drop it from the model. -Jorge -- *De:* Lars M. Rimol lari...@gmail.com *Para:* FS maling list freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal Rusiel jbernal0...@yahoo.es *Enviado:* Miércoles 17 de diciembre de 2014 9:42 *Asunto:* [Freesurfer] Fwd: comparing lme models Hi Jorge, I have fitted two lme models that are identical except that one has age and the other has age². When choosing between the models, comparing lreml seems relevant. However, the lreml + chi square test method in FreeSurfer's lme module is meant for comparing full vs. reduced models, so this is not a typical a case for that. Looking at the lreml maps for the two models, I see that in some regions the age model gives a better fit and in other regions the opposite is true. I created difference maps (lreml_age² - lreml_age) and attached figures to illustrate this. In some regions (blue) the model with age yields a higher lreml and in some regions (red) the model with age² yields a higher lreml. Based on this, can I conclude that I might as well use the model with the linear age term? Or should I perform significance tests comparing the lreml maps even if though aren't nested? Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] white matter snr
Hi, I would like to know whether it is a good idea to use the snr measure from *wm-anat-snr *as a covariate in lme (or glm) analyses? I find significant effects of snr on cortical area and thickness. Am I right in thinking I should be more cautious about interpreting findings in regions where wm snr has a strong/significant effect on the dependent variable? Also, if I use it in an lme model, would it be permissible to use it as a random factor? And finally, is there any similar snr measure for gray matter? (There is of course a wm/gm contrast measure but it is not very thoroughly documented.) Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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 interpret a change in area of 0.004 mm² per year?
Hi Martin, Does that mean that one would expect to see reduced lgi (local gyrification index) where this occurs? Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Wed, Oct 29, 2014 at 3:39 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Lars, two thoughts that came up reading this thread: - each vertex has usually more than 3 triangles (your first mail), the number differs depending on where you are. With a uniform mesh you'd have nearly 60 degree angles so you'd have approx 6 triangles at a vertex. - wm volume can increase when area shrinks. If especially the slucii move further outside the whole surface gets more spherical, decreasing area, but increasing volume. Best, Martin On 10/29/2014 08:44 AM, Bruce Fischl wrote: Hi Lars yes, it seems plausible, particularly since it is so universal. cheers Bruce On Wed, 29 Oct 2014, Lars M. Rimol wrote: Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface. To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that. In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample. Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface, and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects. On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area? As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer: I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model. Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway Bruce Fischl Sat, 06 Sep 2014 07:00:14 -0700 Hi Lars which surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasing cheers Bruce On Sat, 6 Sep 2014, Lars M. Rimol wrote: Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: intercept(random effect) + centered age + group + group x centered age + sex I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface. To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that. In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample. Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface, and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects. On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area? As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer: I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model. Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway Bruce Fischl http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Bruce+Fischl%22 Sat, 06 Sep 2014 07:00:14 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140906 Hi Lars which surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasing cheers Bruce On Sat, 6 Sep 2014, Lars M. Rimol wrote: Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: intercept(random effect) + centered age + group + group x centered age + sex I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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. yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Mon, Oct 27, 2014 at 9:59 AM, Lars M. Rimol lari...@gmail.com wrote: Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface (attached p-maps: lh_0
[Freesurfer] lgi mris_preproc
Hi, In the wiki page on the gyrification index it says that to sample the results to ico, use recon-all -s my_subject_id -qcache -measure pial_lgi If I prefer not to use qudec, can I instead use mris_preproc to do the registration to atlas and concatenate the files and then use mri_surf2sruf to smooth? And then proceed with inferential statistics? Thank you! --- from the wiki: The primary output file is ?h.pial_lgi, which can be viewed as an overlay in tksurfer or freeview: tksurfer my_subject_id lh inflated -overlay lh.pial_lgi To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage': recon-all -s my_subject_id -qcache -measure pial_lgi Do this for each of the subjects in your group -- yours, Lars M. Rimol, PhD Norwegian University of Technology and Science (NTNU) Trondheim, Norway ___ 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] problem with mris_preproc
Hi, I get the following error message when running mris_preproc, and I'm wondering what file is it looking for?: Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file This subject, 007, seems to have all the files it should: [rimol @ ~/subjects/long/long_v0v2_amd]$ ls /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf lh.area lh.inflated.H lh.pial_lgi lh.smoothwm.K1.crv lh.thicknessrh.avg_curv rh.orig rh.smoothwm.BE.crv rh.smoothwm.S.crv rh.white lh.area.mid lh.inflated.K lh.pial-outer-smoothed lh.smoothwm.K2.crv lh.volume rh.curv rh.orig_pialrh.smoothwm.C.crv rh.sphere lh.area.pial lh.jacobian_white lh.smoothwm lh.smoothwm.K.crv lh.w-g.pct.mgh rh.curv.pial rh.orig_white rh.smoothwm.FI.crv rh.sphere.reg lh.avg_curv lh.origlh.smoothwm.BE.crv lh.smoothwm.S.crv lh.whiterh.inflated rh.pial rh.smoothwm.H.crv rh.sulc lh.curv lh.orig_pial lh.smoothwm.C.crv lh.sphere rh.area rh.inflated.H rh.pial_lgi rh.smoothwm.K1.crv rh.thickness lh.curv.pial lh.orig_white lh.smoothwm.FI.crv lh.sphere.reg rh.area.mid rh.inflated.K rh.pial-outer-smoothed rh.smoothwm.K2.crv rh.volume lh.inflated lh.piallh.smoothwm.H.crv lh.sulc rh.area.pialrh.jacobian_white rh.smoothwm rh.smoothwm.K.crv rh.w-g.pct.mgh Here's the entire output: -- [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long ~/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh nsubjects = 172 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.11745 /cluster/home/rimol/subjects/long/long_v0v2_amd Log file is test_pial.mris_preproc.log Thu Sep 18 17:23:19 CEST 2014 setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd cd /cluster/home/rimol/subjects/long/long_v0v2_amd /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh Linux login-0-1.local 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.11745 Src lh sphere.reg Trg lh sphere.reg --- #@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 -- --- mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 007v2.long.007_base srcval = (null) srctype= curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg Loading source data Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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 interpret a change in area of 0.004 mm² per year?
Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: *intercept(random effect) + centered age + group + group x centered age + sex* I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] proportion of surface area of significant region
Thanks, Doug! So I tried this method using fsaverage/surf/lh.white.avg.area.mgh. The results seem to be reasonably consistent with the ones I get when eyeballing the p-maps overlayed on fsaverage in tksurfer. Would you agree that's a reasonable sanity check? When I compare the results to just counting vertices, there doesn't seem to be a huge difference between proportion of #vertices and proportion of surface area. So either there isn't a lot of variance in the sizes of the faces, or the variance is evenly distributed. Finally, if I want to convert from an individual map or the cohort mean map to mm² units, can I do it by scaling the ico area vertex values by the ratio between native and ico total area? So: (vertex value from mean cohort map * total area for cohort mean map) / total area for fsaverage/surf/lh.white.avg.area.mgh, where total area would be the sum of all vertex values? Thank you! LMR --- You don't want to get the surface area from the faces of fsaverage. Instead use the values in fsaverage/surf/lh.white.avg.area.mgh (this is the average of the group used to create fsaverage), or, probably better, get an average area map for your cohort doug On 07/30/2014 08:38 AM, Lars M. Rimol wrote: Hi Bruce, I would like to be able to tell what proportion of a region of interest (ROI), as defined in atlas space by e.g. Desikan-Killiany, that shows a significant effect (based on a p-map). For now I overlay the p-map on the inflated surface of fsaverage in tksurfer and eyeball the proportion. Given a p-map, if I find the FDR threshold and identify the vertices within a given ROI that have a p-value greater than the threshold, then I can find the proportion of the ROI that is suprathreshold. E.g., I find 1986 suprathreshold vertices in bankssts out of 2137, so 93% of vertices in bankssts show a significant effect. My question is: Does that tell me anything about what proportion of the ROI's surface area is affected in atlas space? Obviously, if the faces were uniform, there would be a 1 to 1 relationship between #vertices and area. In the original tesselation of any dataset the size of the faces is uniform, but that changes with topology fix and deformation. I assume that is true also for fsaverage? (so I can't assume [#sig vertices] / [# tot vertices] == the proportion of the ROI's area that is significant in atlas space) I can find the surface area of the suprathreshold region for my sample (or any subset thereof) by looking at a mean area map. But I'm unsure how to do that for fsaverage itself? Is there information on regional surface area directly available? Or would using getFaceArea.m or getFacesArea.m or similar functions be a solution? Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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_cor2label revisited
Hi Doug, Yes that works! I'm viewing it on the surface. LMR On Tue, Jul 15, 2014 at 6:27 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Are you trying to view it in the volume or the surface? When I run freeview viewing the surface and load the label using the Load Label button (not File-LoadLabel), it works for me. Can you try the tksurfer command below? It runs for me. You can ignore the warning about 0 nonzero vertices since they are all set to 1. tksurfer fsaverage lh inflated -label ~/tmp/lh_binarymap_area_covar8.label subject is fsaverage hemiis lh surface is inflated surfer: current subjects dir: /autofs/cluster/con_009/users/ greve/ixi-subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/cluster/con_009/users/greve/ixi-subjects/ixi320/mri checking for nofix files in 'inflated' Reading image info (/autofs/cluster/con_009/users/greve/ixi-subjects/ fsaverage) Reading /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/ mri/orig.mgz surfer: Reading header info from /autofs/cluster/con_009/users/ greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) loading label /homes/4/greve/tmp/lh_binarymap_area_covar8.label reading white matter vertex locations... 0 nonzero vertices found label stat field identically zero - setting to 1 surfer: using interface /autofs/space/tanha_002/users/ greve/fsdev.build/tktools/tksurfer.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_ common.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_ wrappers.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/lib/tcl/ fsgdfPlot.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/ tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... On 07/15/2014 09:04 AM, Lars M. Rimol wrote: Hi, I go to File - Label - load label and there I pick lh_binarymap_area_covar8.label and then I get the error message: % 0 nonzero vertices found label stat field identically zero - setting to 1 That's it! I don't know, but it seems to be saying that all vertices are zero, doesn't it? When I cat the file, I see this: 163839 -34.195 -22.897 -24.093 0.00 163840 -34.295 -23.062 -23.449 0.00 163841 -35.093 -23.358 -22.788 0.00 The leftmost column surely is vertex number, I don't know what the next two are (if this were a volume, I'd say x,y,z coordinates) and if the final column is the value of each vertex, I would have to agree with tksurfer that there are no nonzero vertices. When I load the mgh file, thogh, it has some zero vertices and 98877 that are 100, that is they are larger than 99.992. size(find(gt(testing,99.992))) ans = 98877 1 Here's the code I used to make the binary map and save it as an mgh file: log10pID = significance threshold binaryVLBWlhcovar8(find(gt(binaryVLBWlhcovar8,log10pID))) = 100; binaryVLBWlhcovar8(find(lt(binaryVLBWlhcovar8,log10pID))) = 0; fs_save_mgh(binaryVLBWlhcovar8,'lh_binarymap_area_covar8.mgh',mri); So mri_cor2label must be changing some of these vertices from 99.9etc. to 0, right? LMR On Mon, Jul 14, 2014 at 7:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It loads ok for me both in 5.1 and 5.3. Can you give more info on what is going wrong with tksurfer? On 07/13/2014 05:35 AM, Lars M. Rimol wrote: Hi Doug, I'm having some problems with the label creation again. When I run mri_cor2label, it seems OK (please see below), but when I try to open it in tksurfer, it gives me an error message (bottom). Would you mind taking a look at this label to see what's wrong with it? I'm attaching the binary mgh file and the label. NB! The binary .mgh file is from matlab, where I have set all suprathreshold vertices to 100 and all others to 0. Of course, Matlab doesn't really do this, it sets them to somewhere close to 99.992. I don't suppose I could use greater than 99 in mri_cor2label? # creating label: [LMR in ~ ] mri_cor2label --i /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_ pmaps/lh_binarymap_area_covar8.mgh --id 100 --l /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_ pmaps/lh_binarymap_area_covar8 --surf fsaverage lh $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri
Re: [Freesurfer] Correlation coeffecient
Hi Doug, A naive question in regard to the issue brought up by Chris (see below): Could one simply use this formula (with the F from the GLM for a given contrast): r² = F/(F+df) ? LMR try this oneftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m On 07/11/2014 01:51 PM, Chris Wertz wrote: Hi Freesurfer experts I am trying to obtain correlation coefficients for significant clusters and found a previous post about this, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html but the MATLAB function link within this post is dead? any help is greatly appreciated thanks, Chris -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] create label from binary .mgh file {Disarmed}
Hi Doug, That works! Thanks! I don't know why it didn't the first time (I can't find the old command line). But this command line works (in case anybody else wants to do the same thing): [LMR in ~ ] mri_cor2label --i /home/lmr/ANALYSIS/binary_pmaps/lh_binarymap_area_covar8.mgh --id 1 --l /home/lmr/ANALYSIS/binary_pmaps/lh_binarymap_area_covar8 --surf fsaverage lh LMR Douglas N Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+N+Greve%22 Fri, 11 Jul 2014 11:02:38 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140711 use mri_cor2label with the --surf option On 07/11/2014 01:36 PM, Bruce Fischl wrote: Hi Lars this would be pretty simple to do in matlab, but I'm not sure if we have anything do to it otherwise (Doug might) cheers Bruce On Fri, 11 Jul 2014, Lars M. Rimol wrote: Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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. - Previous message http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html - View by thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#36917 - View by date http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html#36917 - Next message http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36915.html - [Freesurfer] create label from binary .mgh file http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36913.html Lars M. Rimol - - Re: [Freesurfer] create label from binary .mgh file http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html Bruce Fischl - - Re: [Freesurfer] create label from binary .mgh fi... Douglas N Greve Reply via email to [image: The Mail Archive] http://www.mail-archive.com/ - The Mail Archive home http://www.mail-archive.com/ - freesurfer - all messages http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ - freesurfer - about the list http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/info.html - Previous message http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html - Next message http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36915.html -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] create label from binary .mgh file
Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] Linear Mixed Models in FS?
Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only includes numbers from the control-group. Applying the contrast [0 1 0 0 0] to this model, would this not be more appropriate for consider the effect of [centered age] on the control-group alone? Given your previous answers I suspect I'm missing something here, but I would greatly appreciate if you could please take the time to explain to me how I've gone wrong. Thanks! LMR --- Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age?(might be a random effect too)?+ ?Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(random effect) + centered age + group + group x centered age + sex the fourth coefficient is the interaction term that represents the difference in slope between the patient and control groups. This is easy to see from your Question 1 equations. It's also easy to see from those equations that [0 1 0 0 0] tests the effect of time in the control group since the group-specific slope is only equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] problems with cortical surface area maps
Hi Anderson, Thank you! How would you suggest I address this issue when I smooth these images before statistical analysis? I normally use the smoothing algorithm implemented in FreeSurfer (mri_surf2surf). -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] Per-vertex regressors
Hi all, I want to use the --prv (per vertex regressors) option in mri_glmfit, but there is very little information in the Wiki and I couldn't find any relevant info in the mailing list. I have two .mgz files, one contains the dependent variable, the other is the source of my pvr. I tried loading one column from the second file and appending it to the design matrix in Matlab for each vertex (in a loop), but it's too time consuming to be feasible. Someone tipped me about the pvr option in mri_glmfit but from the Wiki (see below) it seems I would have to load the regressors individually here as well..? What is pvr1, pvr2 etc. in the example below? Text files? That's either going to be one very long command line or I have to use a loop here too (probably in Matlab). Is there any way to tell mri_glmfit. for each vertex in the dependent variable file, take the corresponding vector from the pvr-file and append it to the design matrix? [from the WIki:] --pvr pvr1 --prv pvr2 ... Per-voxel (or vertex) regressors (PVR). Normally, the design matrix is 'global', ie, the same matrix is used at each voxel. This option allows the user to specify voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components. Thank you! -- yours, Lars M. Rimol, PhD Division of Mental Health and Addiction Institute of Clinical Medicine University of Oslo P.O. Box 85 Vinderen, 0319 Oslo, Norway ___ 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] residuals exactly zero
Hi, We have experimented a little with different ways of computing the p-values in a GLM analysis based on FreeSurfer data. The way the Matlab reference implementation (fast_fratio.m) handles a situtation where the residuals are exactly zero, seems to be to set those vertices to F = 0 and p = 1. Is this correctly understood? Is this also the case in the underlying C-code? Thank you! LMR -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error message in mri_concat: fp==0
Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error message in mri_concat: fp==0
Hi Bruce, Yes I can create files. I was trying to run a script with almost 500 mgh files that I wanted to concatenate. I figured there was something wrong with the script because I could run command lines to concatenate 10-20 files from that list in the terminal (all 500 files was too much to copy and paste). So I made a new text file with the same contents as the original script (copy and paste) and now it runs just fine. Not sure why, but the script file was originally a text file from Windows so maybe there was some kind of hidden formatting? Thank you! LMR On 20/01/2011, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lars do you have write permission? Is the partition full? Try: touch /home/lmr/test.mgh and see if that works cheers Bruce On Thu, 20 Jan 2011, Lars M. Rimol wrote: Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR 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. -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error message in mri_concat: fp==0
cputime,filesize,datasize,memoryuse,vmemoryuse: unlimited stacksize 10240 bytes coredumpsize 0 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 137216 yours, LMR On 20/01/2011, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I see. Maybe there are too many open file descriptors? If you type 'limit' what does it tell you? On Thu, 20 Jan 2011, Lars M. Rimol wrote: Hi Bruce, Yes I can create files. I was trying to run a script with almost 500 mgh files that I wanted to concatenate. I figured there was something wrong with the script because I could run command lines to concatenate 10-20 files from that list in the terminal (all 500 files was too much to copy and paste). So I made a new text file with the same contents as the original script (copy and paste) and now it runs just fine. Not sure why, but the script file was originally a text file from Windows so maybe there was some kind of hidden formatting? Thank you! LMR On 20/01/2011, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lars do you have write permission? Is the partition full? Try: touch /home/lmr/test.mgh and see if that works cheers Bruce On Thu, 20 Jan 2011, Lars M. Rimol wrote: Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR 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. -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error message in mri_concat: fp==0
stacksize 10240 kbytes, sorry! -- yours, Dr. Lars M. Rimol ___ 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] corpus callosum coordinates
Hi, We are planning to do shape analysis of the corpus callosum. In order to do that we need the coordinates (x,y,z) of the voxels comprising the cc in the subcortical segmentation. We are using FS v. 3.0.2. The corpus callosum info in the aseg.stats shows all zeros for all subjects, does that mean that cc is not identified in 'aseg.mgz' in FS v. 3.0.2? There is corpus callosum info in the aparc.stats files but we assume that's from the cortical surface reconstruction and therefore not appropriate. Do any of the later versions of FS have the information we need in order to identify the corpus callosum in the volumetric segmentation? We know that v. 4.0.0 (and up) have a corpus callosum segmentation with five labels in 'aseg.mgz'. Does that mean that if we redid the recons with this version we would be able to obtain the coordinates of the cc? Is there any way to get this info from the data recon'ed with v3.0.2? Thank you! yours, Dr. Lars M. Rimol ___ 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] cannot read file as type 3
Hi, What does it mean when mris_surf2surf produces the error message that the input file cannot be read as type 3 ? The file is an .mgh which I converted from an .mgz using mri_convert (mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz file. Thank you! yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] cannot read file as type 3
Yes, I can load it as an overlay in tksurfer. Here's the mri_info output: [...@localhost area]$ mri_info TOP_sm100_lh_cc2_11072009.mgh Volume information for TOP_sm100_lh_cc2_11072009.mgh type: MGH dimensions: 163842 x 1 x 1 x 216 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 163842.000 dof: 1 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 216 ras xform present xform info: x_r = 1., y_r = 0., z_r = 0., c_r = 81921. : x_a = 0., y_a = 1., z_a = 0., c_a = 0.5000 : x_s = 0., y_s = 0., z_s = 1., c_s = 0.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. voxel-to-ras determinant 1 ras to voxel transform: 1. -0. -0. -0. -0. 1. -0. -0. -0. -0. 1. -0. 0. 0. 0. 1. PS! I originally had this file (TOP_sm100_lh.mgh), which I reduced in Matlab, i.e. I removed 150 of the 366 subjects and then saved the new matrix with save_mgh. Both the original file and the new one crash in msi_surf2surf, both are viewable in tksurfer and their mri_info info looks similar to me. [...@localhost area]$ mri_info TOP_sm100_lh.mgh Volume information for TOP_sm100_lh.mgh type: MGH dimensions: 163842 x 1 x 1 x 366 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 163842.000 dof: 1 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 366 ras xform present xform info: x_r = 1., y_r = 0., z_r = 0., c_r = 81921. : x_a = 0., y_a = 1., z_a = 0., c_a = 0.5000 : x_s = 0., y_s = 0., z_s = 1., c_s = 0.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. voxel-to-ras determinant 1 ras to voxel transform: 1. -0. -0. -0. -0. 1. -0. -0. -0. -0. 1. -0. 0. 0. 0. 1. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] cannot read file as type 3
Hi Bruce, Yes, mri_info works on all these files, and it states that it's an mgh file and the dimensions look allright and it says: type FLOAT (3). Here's the output for the left hemisphere (with command line) [...@localhost area]$ mri_surf2surf --s fsaverage --sval /home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh --hemi lh --fwhm 30 --tval /home/lmr/subjects/analysis/TOP_sm100.s30_lh_cc2_11072009.mgh srcsubject = fsaverage srcval = /home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh srctype = trgsubject = fsaverage trgval = /home/lmr/subjects/analysis/TOP_sm100.s30_lh_cc2_11072009.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 30 label-src = (null) label-trg = (null) Reading source surface reg /home/lmr/subjects/fsaverage/surf/lh.sphere.reg Loading source data mghRead(/home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh, -1): could not open file ERROR: could not read /home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh as type 3 yours, LMR Date: Sat, 11 Jul 2009 13:42:03 -0400 From: fis...@nmr.mgh.harvard.edu To: lari...@gmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot read file as type 3 Hi Lars, can you send us the whole command line and output? I think type 3 is an MGH/MGZ file. Does mri_info work on it properly? cheers Bruce On Sat, 11 Jul 2009, Lars M. Rimol wrote: Hi, What does it mean when mris_surf2surf produces the error message that the input file cannot be read as type 3 ? The file is an .mgh which I converted from an .mgz using mri_convert (mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz file. Thank you! yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fdr thresholds in tksurfer compared to Nichol's function
Hi, I've used the fdr function in tksurfer and compared the results to Tom Nichol's matlab function (http://www.sph.umich.edu/~nichols/FDR/). I use p = 10.^-abs(pfile), where pfile is 'sig.mgh'. I find that the p-threshold (pID, assuming positive dependence) is usually exactly the same as the one in tksurfer (probably because you use the same algorithm..?). But in some cases where pID is empty, which should mean that there is no suprathreshold vertex, I do get a threshold in tksurfer. Here's an example: For one contrast where pID was returned empty in Nichol's matlab function, I got a threshold of 1.927741 in tksurfer. Is this supposed to happen? The output is: MRISfdr2vwth(rate=0.05000, sign = 0, 1, only marked = 0) = 1.927741 surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 1.927741 Thank you! yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] RE: fdr thresholds in tksurfer compared to Nichol's function
Hi, Please disregard my previous mail. I was a little too trigger happy..., the 1.928 threshold set by tksurfer is too high for any vertex to survive so the two methods DO concur. I should actually look at the maps and not just the output... The reason I asked is that I'm combining images to obtain an overall FDR, either for both hemispheres or for several comparisons. I don't see how this can be done in tksurfer so I'm using Nichols' function, which works just fine. I just don't know how to get an FDR threshold when no vertex has a p-value that survives - but tksurfer obviously produces such a threshold. How do I obtain that threshold? (Or is it simply set just higher than the highest -log(p-value) in the image, for display purposes? It seems always to be just above.) thanks (and apologies for the confusion), LMR From: lari...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: fdr thresholds in tksurfer compared to Nichol's function Date: Thu, 25 Jun 2009 14:07:08 +0200 Hi, I've used the fdr function in tksurfer and compared the results to Tom Nichol's matlab function (http://www.sph.umich.edu/~nichols/FDR/). I use p = 10.^-abs(pfile), where pfile is 'sig.mgh'. I find that the p-threshold (pID, assuming positive dependence) is usually exactly the same as the one in tksurfer (probably because you use the same algorithm..?). But in some cases where pID is empty, which should mean that there is no suprathreshold vertex, I do get a threshold in tksurfer. Here's an example: For one contrast where pID was returned empty in Nichol's matlab function, I got a threshold of 1.927741 in tksurfer. Is this supposed to happen? The output is: MRISfdr2vwth(rate=0.05000, sign = 0, 1, only marked = 0) = 1.927741 surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 1.927741 Thank you! yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FDR correction
Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-values, I get 6 different tresholds: comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) There are lots of significant vertices in comparison 1 and nothing significant, after correction, in comparison 3. Is there anything wrong with using different tresholds here, and concluding that in comparison 1 there were extensive differences between the groups, whereas in comparison 3 there were none? I'm not sure if this is a problem, but I'm afraid some reviewers might have an issue with it. Across the hemispheres, I can choose a conservative threshold which covers both hemispheres, i.e. lower than both the FDR-adjusted treshold for lh and rh. But between the comparisons the tresholds differ even more, by a factor of 10 and 100. And if I choose the most conservative of all the adjusted thresholds, I'm afraid that I'll make a type II error in comparison 1. From what I understand, the adjusted threshold for comparison 3 is more conservative because of the actual empirical data (the distribution of p-values), so that's an empirical argument for using a more conservative threshold there. And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole thing, would that be a better approach? And does Freesurfer use the Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all three p-maps? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] FDR correction
Well, I believe there is a problem in principle here. FDR deals with multiple comparisons across the surface (or brain volume), but how do you deal with a series of such analyses? Of course, if you use a different method of correction you avoid this problem but that's not the point. LMR Date: Tue, 24 Mar 2009 14:03:46 -0300 Subject: Re: [Freesurfer] FDR correction From: p...@netfilter.com.br To: lari...@gmail.com CC: freesurfer@nmr.mgh.harvard.edu Some links that may be helpful: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysishttp://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons Hope it helps. PPJ--- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom On Tue, Mar 24, 2009 at 12:38, Lars M. Rimol lari...@gmail.com wrote: Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-values, I get 6 different tresholds: comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) There are lots of significant vertices in comparison 1 and nothing significant, after correction, in comparison 3. Is there anything wrong with using different tresholds here, and concluding that in comparison 1 there were extensive differences between the groups, whereas in comparison 3 there were none? I'm not sure if this is a problem, but I'm afraid some reviewers might have an issue with it. Across the hemispheres, I can choose a conservative threshold which covers both hemispheres, i.e. lower than both the FDR-adjusted treshold for lh and rh. But between the comparisons the tresholds differ even more, by a factor of 10 and 100. And if I choose the most conservative of all the adjusted thresholds, I'm afraid that I'll make a type II error in comparison 1. From what I understand, the adjusted threshold for comparison 3 is more conservative because of the actual empirical data (the distribution of p-values), so that's an empirical argument for using a more conservative threshold there. And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole thing, would that be a better approach? And does Freesurfer use the Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all three p-maps? Thank you! -- yours, LMR ___ 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
[Freesurfer] homologous lh and rh labels
Hi, This is perhaps a tricky problem. I have created a lh STG label using custom fill and the up to functional threshold option and retrieved the data from those vertices. This label is just a minor portion of the entire STG parcellation. Now I would like to compare to the homologous area in the right hemisphere. Short of using the annotation labels and thereby chosing the entire parcellation, is there any way to get the vertex numbers for the same area in the right hemisphere? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Destrieux or Desikan/Ron Killiany
Hi, I just mapped these on the fsaverage lh.inflated. By images of the folding patterns, do you mean pial or smoothwm images from fsaverage? Or do you mean data from single subjects? LMR Date: Tue, 10 Mar 2009 08:01:31 -0400 From: fis...@nmr.mgh.harvard.edu To: lari...@gmail.com CC: freesurfer@nmr.mgh.harvard.edu; destri...@med.univ-tours.fr; ra...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Destrieux or Desikan/Ron Killiany Hi Lars, you need to send images of the folding patterns for Christophe and Rahul to decide. cheers, Bruce On Tue, 10 Mar 2009, Lars M. Rimol wrote: Hi, I have an area of significance on the mesial surface of the hemisphere (please see attached tiffs). I would like to know if it is exclusively in the cingulate or in cingulate and SFG. The prolbem is that the two atlases don't agree. The upper more than half of this significant area is in SFG according to lh.aparc.annot and in cingulate gyrus and sulcus according to lh.aparc.a2005s.annot. I know there have been some issues before with cingulate and SFG in the Destrieux atals ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05399.html) but it's unlcear to me whether these have been resolved. As you can see from the tiffs, in lh.aparc.annot the significant area is inside the corpus callosum (a small part), caudal and rostral ant. cingulate, and SFG. In lh.aparc.a2005s.annot it is inside pericallosal sulcus, g. cingulate main part, s. cingulate main part, and only a very small part of it extends into SFG. These are substantially different interpretations. Is one atlas more accurate in this region? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Destrieux or Desikan/Ron Killiany
Hi Rahul, Thanks for the input! I'm afraid I don't see how the atlases agree with regard to the medial SFG, since only a tiny portion of the area of interest is in SFG according to the Destriuex annotation (SFG is the uppermost parcellation in the anterior half of the hemisphere in that image). So whether or not it extends into the SFG would change with just a slight change in smooting kernel. Thank you! LMR Date: Tue, 10 Mar 2009 08:12:08 -0400 Subject: Re: [Freesurfer] Destrieux or Desikan/Ron Killiany From: ra...@nmr.mgh.harvard.edu To: lari...@gmail.com CC: freesurfer@nmr.mgh.harvard.edu Hi Lars, From looking at the images you sent, your area of interest is clearly in the anterior portion of the cingulate gyrus as well as in the medial portion of the superior frontal gyrus (as well as a small portion in the corpus callosum). I think both atlases agree on this quite consistently. Hope this helps. Best, Rahul -- Rahul S. Desikan ra...@nmr.mgh.harvard.edu Hi, I have an area of significance on the mesial surface of the hemisphere (please see attached tiffs). I would like to know if it is exclusively in the cingulate or in cingulate and SFG. The prolbem is that the two atlases don't agree. The upper more than half of this significant area is in SFG according to lh.aparc.annot and in cingulate gyrus and sulcus according to lh.aparc.a2005s.annot. I know there have been some issues before with cingulate and SFG in the Destrieux atals ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05399.html) but it's unlcear to me whether these have been resolved. As you can see from the tiffs, in lh.aparc.annot the significant area is inside the corpus callosum (a small part), caudal and rostral ant. cingulate, and SFG. In lh.aparc.a2005s.annot it is inside pericallosal sulcus, g. cingulate main part, s. cingulate main part, and only a very small part of it extends into SFG. These are substantially different interpretations. Is one atlas more accurate in this region? Thank you! -- yours, LMR ___ 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
[Freesurfer] effect sizes and SE
Hi, Is there a way to get the standard error of the adjusted means for each group in a glm with a categorical predictor? -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] standard error for betas
Hi, I have fitted a glm with three different groups, using mri_glmfit (FS v4.0.3). I use the beta.mgh to get the adjusted means within an ROI, for each group. I'd like to make a bar or box diagram with the adjusted means/betas, but I'm not sure how to get the standard error of the betas so I can make error bars or a confidence interval. It seems that mris_anatomical_stats won't take the beta.mgh as input. Is there another way to do this in FS? Or will I have to do it outside FS? All my contrasts have only one vector, so each comparison should reduce to a t-test (according to the Wiki). In general, given the p (sig.mgh) and df of a t-test, I can get the t-value, and given the difference between the betas, the df and the t, I can get the SE. But I assume this is a little more complicated than that? I guess I can't use the rvar.mgh or rstd.mgh, since these are based on the whole model and not just the two groups. Which brings me to a related question: In mri_glmfit, when you have more than two groups in your model, and perhaps also e.g. age as a continuous regressor, and you set a contrast to compare two of the groups, does the variance estimate (SE) include the variance of all the variables, i.e. all groups that are in the model including the ones not included in the comparison + whatever covariates there may be? If so, isn't it really closer to a Tukey's or Scheffe's than an ordinary t-test? But back to my main question: Is there a way to get a measure of dispersion or confidence for the betas associated with each of the three groups in my analysis? (And if there is, I probably can't just average that measure across all vertices in the ROI, right?) Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] getting vertex numbers
Hi, I've done a glm model fit comparing cortical thickness between two groups, and have certain areas (blobs) on the cortical surface that are above sig. threshold. I'd like to get a list of the vertex numbers for each of these significant areas, which do not correspond to the parcellations in FS. In other words, I'm not trying to combine the already excisting ROI's. I've tried drawing labels (on fsaverage) and saving them, but without success. I clicked on 'Make path' and tried to mark vertices around the area, then I tried 'Custom fill' with various options, and 'Mark label', 'New label from marked' and 'save label'. But I only manage to save one or at most 3-4 vertices. I'm using FS v 4.0.5. Any tip on how to do this would be appreciated! Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freeglut ERROR
Hi, In tksurfer, when I have loaded an overlay and then try to add a color bar, I get this error message: freeglut ERROR: Function glutBitmapCharacter called without first calling 'glutInit' I'm using freeglut v 2.4.0. I don't know if this is caused by a bug in freeglut (I think it's the latest version). Anyone know how to fix this? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer problems
Hi, I am experiencing similar problems to Jennifer and Glenn with tksurfer; the (tksurfer) error message is: surfer: ### redraw failed: no gl window open and the display shows only a thin slice of the posterior of the surface. The computer is a fresh install of RHEL 5 on a new machine, and my university IT department has updated the OS in connection with a Matlab installation. I believe they used run yum update. I have tried both FS v.4.0.3 and v.4.0.4. yours, LMR -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer version 3.0 ?
Hi, We have a dataset that was processed (by somebody else) with an old freesurfer version and we need to find out exactly which version was used. We have a freesurfer_3.0 directory (and a freesurfer-Linux-centos4-stable-v3.0-full.tar.gz download) with a build-stamp.txt that says: freesurfer-Linux-centos4-stable-v3.0 Is the final digit just missing, or was this a version prior to 3.0.1? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] imensions of an mgh file generated by
Hi, I'm just wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used with mris_preproc. But when I run mris_preproc on 300 subjects I get a 163842x1 file (as read in Matlab). Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Dimensions of an mgh file generated by mris_preproc
Hi, I'm wondering what the dimensions of an mgh file generated by mris_preproc with e.g. 300 subjects should be? Should it be 163842x1 or 163842x300 ? I would assume that it should contain a vector for each vertex, with the same length as number of subjects that were listed in the fsgd file used with mris_preproc. But when I run mris_preproc on 300 subjects I get a 163842x1 file (as read in Matlab). Why? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] installation
Hi, I downloaded the freesurfer-Linux-rh9-stable-pub-v4.0.3-full, and I followed the instructions on your website ( http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-release-full.README.txt ): 1) extract to /usr/pubsw/packages/ 2) place the license file in the resulting /usr/pubsw/packages/freesurfer 3) type recon-all --help When I did (3) I got text about FreeSurfer, so far so good, but if I try to start tksurfer og tkmedit, I get: tksurfer.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory mris_preproc mri_surf2surf mri_glmfit all seem to work, i.e. I get the normal help text when I type the commands without any further input What should I do next? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit
Hi, I ran mri_glmfit with a fsgdf looking (in principle) like this: GroupDescriptorFile 1 Title MyTitle Class Group1 plus blue Class Group2 circle green Variables ICV Input subjid1 Group1 1 Input subjid2 Group22 Dependent variable iscortical thickness. When I load group descriptor file, i.e. y.fsgd, and click on a vertex and choose View by class, the button to the right of that has only one level: ICV, and the x axis of the graph also has the title ICV (and units that seem to represent ICV). However, I am interested in visualising the dependent varable cortical thickness per vertex, not the continuous predictor/regressor ICV. Have I made a mistake in the fsgdf? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit
Hi, Please ignore my previous mail, I did not see that external on the y axis means dependent variable (blame it on the early morning blues...) -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject
Hi Bruce, Oh yes, I see that now! And the problem is that FS looks for the FSGDF under SUBJECTS_DIR//space/emc1/3/data/TOP/Analysis_lmr/, but SUBJECTS_DIR and Analysis_lmr are both in the same directory, i.e. /space/emc1/3/data/TOP. I thought that by giving the full path to the FSGDF I had taken care of that: make_average_subject --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest Is there a way around that, or do I have to put the FSGDF inside the SUBJECTS_DIR? The reason I would like to keep them separate is that lab techs are doing scan workups inside the SUBJECTS_DIR, and I don't want to create new directories and files inside there all the time. I guess this is a general question, is it possible to run make_average_subject, mris_preproc and surf2surf and get the FSGDF from a dir that is not a subdirectory of the subjectsdir, and also write the output to that dir? It seems if you give the full path, FS assumes that it should be added to the path of the subjects dir. Thank you! Lars Hi Lars, it looks like no input subjects are defined. Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote: Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t make_average_surface input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average-subject
Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t make_average_surface input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz INFO: extension is mgz [EMAIL PROTECTED] Making rh annotation - Wed Jun 27 18:06:47 PDT 2007 mris_ca_label -ml-annot rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.curvature.buckner40.filled.desikan_killiany.gcs reading color table from GCSA file average std = 35.0 0.3 using min determinant for regularization = 0.011 0 singular and 829 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 376 changed) writing colortable into annotation file... mris_ca_label -ml-annot rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.atlas2005_simple.gcs reading color table from GCSA file average std = 1.0 0.2 using min determinant for regularization = 0.000 0 singular and 827 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1935 changed) writing colortable into annotation file... [EMAIL PROTECTED] Making average rh.orig surface - Wed Jun 27 18:07:06 PDT 2007 /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mris_make_average_surface -i 7 -o orig -sdir-out /space/emc1/3/data/TOP/Containers rh orig_avg sphere.reg/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest reading vertex positions from orig... mris_make_average_surface [options] hemi outsurfname cansurfname outsubject subj1 subj2 subj3 ... Run with -help for more info -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] color coding for parcellations/regions of interest
Hi, I have combined the Desikan parcellations into regions of interest, which I would like to visualize. So I need to create an ad hoc color coding scheme. In order to visualize the ROIs I would load a file equivalent to the ?h.aparca2005s.annot file, which would show the same color for those parcellations that belong to one and the same ROI. Which file contains those color definitions, or in other words which file do I need to modify in order to be able do that? Tank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_preproc
Hi, When I try to run mris_preproc wiht the nocleanup flag I get an error message: flag --nocleanup not recognized Same thing happens for --cleanup (i.e., not recognized), and --tmpdir tmpdir doesn't seem to work (it still does cleanup). But all these flags are listed under the help function for mris_preproc: --tmpdir dir : use tmpdir. Implies --nocleanup. --nocleanup : do not delete tmpdir --cleanup : delete tmpdir (default) I'm using /RH4-x86_64-R302. Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_concat
Hi, I am wondering if it is possible to use some kind of a list of subjects to specify input for mri_concat, like you can use --f filename, where filename refers to a list of subjects, for mri_surf2surf ? It seems that using e.g.: mri_concat subj*-lh.mgz --o allsubjs-lh.mgz is an alternative to: mri_concat subj1-lh.mgz subj2-lh.mgz ... subjN-lh.mgz--o allsubjs-lh.mgz but if you have a typical Freesurfer subjects directory where the files you want to concatenate are buried in e.g. the surf directory of each subject, it would be very useful to be able to specify a list of subjects. The mri_concat --help function doesn't seem to include any such option. Am I missing something, is there an alternative way of doing it? Thank you! -- yours, LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] output from single subject sphere morph to atlas
Hi, Is the determinant of the Jacobian matrix for the sphere morph to atlas space saved vertex by vertex? If so, where is it saved? -- yours,LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] source of thickness information for mris_preproc
Hi, When one runs mris_preproc with e.g. -meas thickness, does it get the thickness information from the files in the stats directory within each subject's directory- or from the ?h.thickness files under the surf directories? Thank you!-- yours,LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject memory issues
Hi, I just ran make_average_subjects with increased swap (from 2G to 8G) on 178 subjects and now it worked, which would seem to indicate that it may have been a memory issue? I did not crash with 3, 10 and 113 subjects with 2G swap. yours, LMR Hmmm, I've run it on 100 subjects without trouble. I'll try now and see if I can replicate locally. Is there anything different about these volumes? Are they all 256^3 and unsigned char? cheers, Bruce Could be a memory leak. Can you send us all the text output? We need to know specifically what program it is dying on. doug Hi, I am analysing a dataset with 180 subjects. When I run make_average_subjects it crashes, the error message usually being something like this: mghRead: encountered error executing: 'zcat /space/monkeys/1/home/lmr /subjects/VETSA_test/testAVG/tmp/make_average_vol-tmp/orig-19963b.mgz',frame -1 I have tried running it with fewer subjects and it worked with 3, 10 and 73 subjects. Also, it crashes at different points in the processing stream, so once it crashed at subject # 130, which I removed from the list of subjects, and then next time it crashed at # 30. My frist guess was that it is a memory problem. I tried running the top command in a different terminal at the same time as running make_average_subject with 2 and 10 subjects, and it seemed to require up to 400m of virtual memory and 10% of memory, but I couldn't see any difference in memory demands between running 2 and 10 subjects. This was running with 4G of physical memory and 2G of swap. Is this a known issue? (Couldn't find anything in the mailing list archive..) Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject
Hi, I have two questions on make_average_subject1) Why are two sets of surfaces created by the make_average_subjectscript? What is the difference between e.g. inflated and inflated_avg?Which one(s) should be used for visualization? 2) As far as I understand, make_average_subject is run for visualization purposes only, and the output is not critical for the integrity of the statistical analyses (recon-all does the spherical warping and registration, and t he mris_preproc script makes sure the tesselation is uniform across the data set). So, does it matter if there are defects in the surfaces created by make_average_subject? I tend to get topological defects in the inflated_avg.Thank you! -- yours,LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] which script creates the design matrix?
Hi, I am using FS v3.02. I am using the tutorial to figure out how to do group analysis with the new FS version but there is one step that is confusing. The tutorial says that I should first create a FSGDF (and run make_average-subject), and then it says that running mris_glm will create the design matrix. But further down on the page it says that that mri_glmfit is replacing mris_glm. So, does that mean that I no longer have to use mris_glm to create the design matrix, and that mri_glmfit will create it? So I should run 1) make_average_subject, 2) mri_preproc and mri_surf2surf, and 3) mri_glmfit? Or does it mean that I should run 1) make_average_subject, 2) glms_mri , 3) mri_preproc and mri_surf2surf, and 4) mri_glmfit? Thank you!-- yours,LMR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach transform with brain.mgz
Hi,We have15 out of16 data sets with Final Objective Function value 0.1. We also find some deviations from the talairach (or MNI) volume when we visually inspect the images (fixed vs. movable) in tkregister2. But we are unsure how large the deviations must be for it to be a problem, so we rely on the Final Objective Function value. When it comes to the intensity normalization, that's even harder to inspect visually, so we don't really know how to check that (unless there are really huge effects). But when we use the brain.mgz image as input for the talairach, the Final Objective Value improves, that's why we've started using that. So we need to know how to proceed from there.(We use the recommended reconstruction, so we check the talairach and skullstrip after autorecon1.) Thanks! -- yours,Lars M. Rimol depends why you needed to improve the talairach. If it's just forreporting purposes and the filling/intensity normalization all workedfine then you don't need to.cheers,Bruce Hi, After having redone mri_convert with an edited brain.mgz as input file, in order to improve the talairach transform, and after having changed the file names (brain.xfm - talairach.xfm), should we then go to autorecon2? (or do we need to re-run some more scripts from autorecon1?) -- yours, Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cerebellum segmentation
Hi Bruce and Satra, Our specific goalisto measure the vermis. It's time consuming to do it manually,so my idea was to ask if it could be possible to develop an automatic segmentation/parcellation procedure, similar to aseg, that includes also the vermis. (In addition, we have three subdivisions of vermis.)I do realize that reconstructing the cerebellar surface is a very difficult task because of the spatial resolution issue but maybe a volumetric approach similar to aseg could be feasible? Hi Satra,we do segment the cerebellum with the aseg stuff into cerebellar gray andwhite. I guess it's a question of what your goals are Lars.-- yours,Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cerebellum atlas
Hi,We have manual tracings of the cerebellum (approx. 100 brains), which were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which file format would be most convenient? Analyze? (The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)-- yours, Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach transform with brain.mgz as input file
Hi, After having redone mri_convert with an edited brain.mgz as input file, in order to improve the talairach transform, and after having changed the file names (brain.xfm - talairach.xfm), should we then go to autorecon2? (or do we need to re-run some more scripts from autorecon1?) -- yours,Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
