Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

eTIV Normalization Issues
by Jason Reed 12 Dec '07

12 Dec '07

Hi all, We want to normalize our data using eTIV and compared the eTIV values generated in aseg.stats to the total brain volume we calculate by summing: 1) Non-cerebral cortex volumes from aseg.stats (including ventricles) 2) Cerebral cortex volumes from lh and rh.aparc.stats We compared eTIV to the total brain volume as calculated above from aseg and aparc.stats for 40 subjects and found that, on average, eTIV is 27% larger. This difference is larger than we expect. Are we missing something? Thank you! Jason

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Phillips 3T
by roberto 12 Dec '07

12 Dec '07

Hi, We are planning to switch to a 3T Philips system and we would like to use FreeSurfer to process our new sequences. Although I have seen the recommendations on the web (http://www.nmr.mgh.harvard.edu/~andre/ <http://www.nmr.mgh.harvard.edu/%7Eandre/>), I was wondering if anyone using a 3T Phillips system could give an idea of a sequence working well in FreeSurfer. Thanks in advance ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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Re: Freesurfer Digest, Vol 46, Issue 29
by Sebastian Moeller 11 Dec '07

11 Dec '07

Hi there, On Dec 11, 2007, at 10:22 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. problem on mri_vol2surf (lan lin) > 2. question about white surface (lan lin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Dec 2007 10:28:15 -0700 > From: "lan lin" <lanlin75(a)gmail.com> > Subject: [Freesurfer] problem on mri_vol2surf > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <a72561a70712110928p66d019acjdbc2f40b2f873e28(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I have tried to map the functional volume onto MRI surface > > functional image has been coregistered with MRI (voxel size is > resample to > same size) > > Here is the command > > mri_vol2surf --reg forig.mgz --trgsubject 003_S_1257 --hemi lh --surf > inflated --surfreg lh.sphere.reg --out lh.fsurf.mgh --srcreg > forig.mgz.reg °°°°°°°°°°°° try --surf white instead of --surf inflated You get what you order, but not what you want. Been there done that, did not like it either ;).. ahoi Sebastian > > forig.mgz is functional image > 003_S_1257 is MRI > > orig.mgz.reg=[003_S_1257 > 1.000000 > 1.000000 > 1.000000 > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 > 0 0 0 1 > round] > > After surface generated, we found that generated surface is smaller > compared > with original MRI. > > Did I make any mistake? > > thanks > Lan >

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question about white surface
by lan lin 11 Dec '07

11 Dec '07

When I used tkmedit and tksurfer to view the same subject, something really confused me. >From tkmedit, the yellow line is white surface, we can find that the generate white surface is clearly wrong. >From tksurfer, when I viewed the white surface, I can't find any problem. Why tkmedit and tksurfer gave me different result on same subject?

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problem on mri_vol2surf
by lan lin 11 Dec '07

11 Dec '07

I have tried to map the functional volume onto MRI surface functional image has been coregistered with MRI (voxel size is resample to same size) Here is the command mri_vol2surf --reg forig.mgz --trgsubject 003_S_1257 --hemi lh --surf inflated --surfreg lh.sphere.reg --out lh.fsurf.mgh --srcreg forig.mgz.reg forig.mgz is functional image 003_S_1257 is MRI orig.mgz.reg=[003_S_1257 1.000000 1.000000 1.000000 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0 0 0 1 round] After surface generated, we found that generated surface is smaller compared with original MRI. Did I make any mistake? thanks Lan

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tkmedit result no activation
by anisha narula 11 Dec '07

11 Dec '07

Hello Doug, I am doing a retinotopy analysis and when I perform the sliceview-sess command, I get activation in the areas of interest. I used the tkmedit-sess command *tkmedit-sess -analysis rtopy -contrast eccen -map h -sf sessid -df sessdir -volid orig.mgz* however there is no activation. I have attached the image above. Thank You

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version
by Feng-Xian Yan 10 Dec '07

10 Dec '07

Hi, I want to use freesurfer to quantify cortical thickness, and I want to use the software under Linux fedora core 4. My computer's equipment is Quad-Core processor Intel Q6600, DDR2 memory 4GB, Sata2 disks 320G, GeFORCE8600. Which version do you recommend? i386? or x86_84? Thanks

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mri_convert problem while unpacking functionals
by Dan Dillon 10 Dec '07

10 Dec '07

Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1 localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3 T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495 to 3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f and save as SUBJ.cfg Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast We get this error when it encounters the first functional run: --------------------------------------------------------- Run 9 ----------------------------------------- Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz)

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conversion
by Anca-Larisa Sandu 10 Dec '07

10 Dec '07

I have a question about conversions. Is it possible to convert a file with the extension ".mgz" from Freesurfer to a file with the extension ".img", which can be read for example in SPM? If it is possible how should I do this conversion? Thank you in advance! Anca Sandu ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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tkmedit-sess error
by anisha narula 10 Dec '07

10 Dec '07

Hello, I am doing a retinotopy study, and when I view the slices using the sliceview-sess command I obtain activation in the regions desired. However, when I view results on the flattened patches, activation is messed up. I tried running the tkmedit-sess command. tkmedit-sess -analysis rtopy -contrast h -map t -sf sessid -df sessdir and it gave me this error: INFO: Found session in: /home/anisha87/freesurfer/subjects//ac1_ret grep: /home/anisha87/freesurfer/subjects//ac1_ret/session.info: No such file ordirectory INFO: Found session in: /home/anisha87/freesurfer/subjects//ac1_ret grep: /home/anisha87/freesurfer/subjects//ac1_ret/session.info: No such file ordirectory -------------------------------------------------------------- tkmedit-sess logfile is /home/anisha87/freesurfer/subjects/ac1_ret_study/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /home/anisha87/freesurfer/subjects INFO: subject is ac1_anatomical INFO: subject is ac1_anatomical ------------------------ SUBJECTS_DIR /home/anisha87/freesurfer/subjects /home/anisha87/freesurfer/subjects/ac1_ret_study tkmedit ac1_anatomical orig -overlay /home/anisha87/freesurfer/subjects/ac1_ret/bold/rtopy/eccen/h_000.bfloat -overlay-reg /home/anisha87/freesurfer/subjects/ac1_ret/bold/register.dat -fthresh 2 -fmid 5 -fslope 1 ------------------------ *corRead(): can't open file /home/anisha87/freesurfer/subjects/ac1_anatomical/mri/orig/COR-.info * * Error: Loading volume orig* Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. tkmedit failed The file located in.the direcotory orig is 001.mgz I can send it if needed. When I run tkmedit for MT localization study for the same subject, I get the same error. Thank You

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