Freesurfer

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30096 discussions

Checking raw dicom files
by qtnguyen＠nmr.mgh.harvard.edu 04 Apr '13

04 Apr '13

Dear Freesurfer experts, After I ran the functional to structural registration using the bbregister command, it looks like the dorsal part of the brain for this participant is cut off in the BOLD images. When we ran the scan, we made sure that the slice prescription covered the entire brain. We also looked at the functional scan in the control room right after the scan and it looked ok. We aren't sure what went wrong and why the bold data is cut off. Is there any way I can look at the raw dicom files to check if it includes the entire brain? Thank you, Trang

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faster wfile reading in matlab
by Keith Jamison 04 Apr '13

04 Apr '13

I noticed it was taking 6-7 seconds to read in a wfile (scalar surface overlay) into matlab using fast_read_wfile.m. In case anybody else finds this annoying, here's a faster alternative that produces identical output: in fast_read_wfile.m, replace everything after the first fread line with: vnum = fast_fread3(fid) ; % Number of non-zero values A = uint32(fread(fid,vnum*7,'uchar')); fclose(fid); v = bitshift(A(1:7:end), 16) + bitshift(A(2:7:end),8) + A(3:7:end); w0 = bitshift(A(4:7:end),24) + bitshift(A(5:7:end),16) + bitshift(A(6:7:end),8) + A(7:7:end); w = zeros(max(v),1); w(v+1) = typecast(w0,'single'); -Keith

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R: Re: R: Re: cortical thickness normalization
by stdp82＠virgilio.it 04 Apr '13

04 Apr '13

I'm sorry. I'm performing the cortical thickness analysis on three groups (2 pathological groups and 1 control group). I'm interested mainly to the differences between the two groups of disease. These are my questions: 1- Is qdec a good option for my study design or I should use other glm option that contains all 3 groups in the same matrix design? 2-As you suggest I'm using always mean cortical thickness as nuisance factor in qdec. If I'd like added 2 or more covariates, is correct if I add each covariate separately in my matrix.dat or I should add all covariates together in my matrix.dat? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 18.23 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: cortical thickness normalization Hi,Sorry, but I don't understand what you're asking. -MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 9:31 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] R: Re: cortical thickness normalization Thank you very much, Michael! I have just an other important question, please. I'm performing cortical thickness analysis on three groups. One of this is a control group and I'm using it as support because I'm interested only to difference between the two groups of disease. These are my questions: 1- Is correct if I'm applying qdec, testing before a) disease 1 vs disease 2; b) controls vs disease 1 and c) controls vs disease 2. 2- Addictionally to cortical thickness that I'm reporting always as nuisance factor in qdec, I'd test some covariates. Taking in account my study design, could I test each covariates separately on my model using qdec? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 15.45 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] cortical thickness normalization If you're studying thickness, I'm a fan of using mean cortical thickness as the covariate (since thickness is what you're studying). I've posted on this in the past. cheers,-MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 7:21 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] cortical thickness normalization Hi list, I'm reading a lot of post on this list about cortical thickness normalization. I' m noting very different results on my data when I use mean thickness or ICV as nuisance factor than no factor. I'm confuse on this topic, could you advise the best way, please? Thanks, Stefano _______________________________________________ Freesurfer mailing list Freesurfer@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 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Permutation doubts
by Gabriel Gonzalez Escamilla 04 Apr '13

04 Apr '13

4 4

Re: [Freesurfer] Projection of markers from the scalp to cortical surfaces
by Douglas Greve 04 Apr '13

04 Apr '13

When you say it does not work, what do you mean? Did it not put the label in the right place? The number of vertices in the output label may be much less than in the input. label2label just finds the vertex that is closest to each label point. A multiple input label points may map to a single output label. doug On 4/3/13 4:24 PM, Eleonora Maggioni wrote: > Dear Doug, > thank you for the suggestion. > I used the new file that you sent me exactly as in the example 4, but > the labels which are effectively translated into the nearest vertex > surface labels are few. > I first selected the marker labels on the T1 image within tkmedit. As > the labels are outside the head volume, I put the maximum distance > --paint as 50 mm, to be sure that the distance is sufficient to find a > surface vertex. But anyway is still does not works. > Can this be due to the external position of the markers? Which kind of > projection is done by mri_label2label? > Thank you for your support! > > Eleonora > > 2013/4/2 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > Hi Eleonora, > > the easiest way to do this is to create a label of the electrodes, > then > use mri_label2label to map them to the nearest pial vertices. This > ability to map volume labels to nearest surface vertices is broken in > the current version. I've fixed this and put a new version here: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2lab… > > Run it with --help and use Example 4. > doug > > > > On 04/02/2013 08:19 AM, Eleonora Maggioni wrote: > > Hi Freesurfer experts, > > I am new to FreeSurfer and I have a question. > > I have markers of EEG electrodes on the T1 image of a subject and I > > want to project them from the scalp to his pial surface (that I > > reconstructed using the standard procedure). > > To do so, I manually selected the central point of each marker in > > tkmedit and I defined a control point. Then I red that control point > > with tksurfer on the corresponding pial surface. This should be the > > projection to the pial surface: is this procedure correct? If > yes, in > > which coordinate system is the projection made? > > Thank you in advance, > > Kind regards, > > > > -- > > Eleonora Maggioni > > > > BioEngineering PhD student > > Politecnico di Milano > > Istituto E.Medea, Bosisio Parini (LC) > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Eleonora Maggioni > > BioEngineering PhD student > Politecnico di Milano > Istituto E.Medea, Bosisio Parini (LC) >

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R: Re: cortical thickness normalization
by stdp82＠virgilio.it 04 Apr '13

04 Apr '13

Thank you very much, Michael! I have just an other important question, please. I'm performing cortical thickness analysis on three groups. One of this is a control group and I'm using it as support because I'm interested only to difference between the two groups of disease. These are my questions: 1- Is correct if I'm applying qdec, testing before a) disease 1 vs disease 2; b) controls vs disease 1 and c) controls vs disease 2. 2- Addictionally to cortical thickness that I'm reporting always as nuisance factor in qdec, I'd test some covariates. Taking in account my study design, could I test each covariates separately on my model using qdec? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 15.45 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] cortical thickness normalization If you're studying thickness, I'm a fan of using mean cortical thickness as the covariate (since thickness is what you're studying). I've posted on this in the past. cheers,-MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 7:21 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] cortical thickness normalization Hi list, I'm reading a lot of post on this list about cortical thickness normalization. I' m noting very different results on my data when I use mean thickness or ICV as nuisance factor than no factor. I'm confuse on this topic, could you advise the best way, please? Thanks, Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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stats question
by j janssen 04 Apr '13

04 Apr '13

Hi, i read the following in a paper and would like to do the same: "At each vertex in each hemisphere, the proportion of total variance in cortical thickness (CT) accounted for by 2 linear regression models was compared: One that did not include an age-by-group interaction term, Model 1: [CT = intercept + (group * b1) + (age * b2)] and one that did, Model 2: [CT = intercept + (group * b1) + (age * b2) + (group * age * b3)]. This resulted in an F ratio map for each hemisphere showing the degree to which the inclusion of an age-by-group term increased the proportion of CT variance that was accounted for." i have set up the matrices for the 2 models. my questions: 1. do you think that i should test the effect of age in model 1 (contrast: 0 0 1) and the effect of age * group in model 2 (contrast 0 0 0 1 -1)? if not, what do you suggest? 2. do you have any idea how to combine these two analyses in a resulting F ratio map? thanks, -joost

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Fwd: Error with experimental design using FSGD
by Joshua deSouza 04 Apr '13

04 Apr '13

Hello Sir/Madam, I am currently running a statistical test using the FSGD method. I am encountering a problem in relation to the creation of the glmdir folder when I run the mri_glmfit function. I recieve an ERROR message that tells me that the design matrix (automatically generated) is ill conditioned or badly scaled, condo = 10565.7. All the steps before creating the glmdir folder have been done in accordance with the FSGD group analysis tutorial on the freesurfer wiki. The command line is : mri_glmfit --y lh.thomas4.10.mgh --fsgd thomas4.txt dods --C t4.txt --surf fsaverage lh --cortex --glmdir lh.thomas4.glmdir The FSGD file = thomas4.txt ( contains 2 groups and 5 variables) The data matrix = Xg.dat The contrast matrix = t4.txt There are 3 columns of variables that have discreet values of either 1 or 2. However I have tried this with another FSGD file (thomas3.txt) that contained 4 variables of which 2 were continous and the other 2 were in 1s' and 2s'. The contrast matrix of thomas3.txt = C.dat The design matrix of thomas3.txt = Xg1.dat I was able to generate a glmdir using mri_glmfit with thomas3.txt and generate a surface for tksurfer to use. The file created was the sig.mgh file which was then compared with the fsaverage files. However once I added another variable titled "voxel" in thomas4.txt, I received the error message. I did a correlation of the columns containing 1s and 2s in the FSGD file thomas4.txt using Matlab and have not found any significant correlation with each other. Please do advise on how to solve this issue and also from where the problem could stem from as I am unsure as to the nature of the problem. Thank You for your patience and assistance Joshua

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Problems with freesurfer after an upgrade to fedora 18
by Sidy Fall 04 Apr '13

04 Apr '13

After doing an upgrade from fedora 17 to fedora 18,I am trying to execute the installation tests, I can't start "$tkmedit", tksurfer or mri_convert. But freeview and qdec seem to be good. Tested with a CentOS4 or a CentOS6 recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $ -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl --------- Linux version 3.8.5-201.fc18.x86_64 (mockbuild@bkernel02) (gcc version 4.7.2 20121109 (Red Hat 4.7.2-8)) processor:Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz tcsh 6.18.00 (Astron) 2012-01-14 -------------------- When I do: tkmedit bert orig.mgz, it returned, ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : ----------------------- When I do: tksurfer bert rh pial, it returned, subject is bert hemi is rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/fallsi/Protocoles checking for nofix files in 'pial' Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz ------------------- When I start mri_convert, I have this error message: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from IM1... Segmentation fault (core dumped) --------------- the contents of .xdebug_tkmedit: tkmedit started: Wed Apr 3 11:43:32 2013 /usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/fallsi/Protocoles Set subject home dir to /usr/local/freesurfer/subjects/bert Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27675600, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00: ---------------------- Thank you in advance,

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mri_robust_register to obtain jacobian
by Jayachandra Raghava 04 Apr '13

04 Apr '13

Hello All, I am trying to use mri_robust_register to compute the symmetric rigid registration for inverse consistency. Is there a way to output the inverse consistent jacobian for the same registration? Thank you, Jay

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