Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

reading DICOM fields
by Michael Harms 13 Dec '07

13 Dec '07

Hello, Will any of the FS utilities read a Siemens DICOM file and dump the (complete) DICOM header information to the terminal or text file? I've looked at the options for mri_info and unpacksdcmdir, but as far as I can tell neither have this capability. We have a handy Sun executable that can do this, but I've tried without success to locate a Linux executable that could do the same. Does anyone out there know of one? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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General editing questions
by Chris Watson 13 Dec '07

13 Dec '07

Hello, I've been looking through the archives and still have some questions about getting the best data for GM volume, WM volume, and the volumes of each sub-cortical structure. This is lengthy, but I'm trying to save a lot of future man-hours that I wasted on the first dataset I was doing. *1)* I ran recon-all -autorecon-all overnight, not knowing that I could make edits in the middle of the process. Does this mean that, e.g if I need to add control points, I have to do / recon-all -autorecon2-cp -autorecon3, /and then make edits to the new wm.mgz and do /recon-all -autorecon2-wm -autorecon3/, *then* make edits to the pial surface and run everything to the end? Or, if I add control points, then only run recon-all -autorecon2-cp, this will be acceptable? And then edit wm.mgz, and run /recon-all -autorecon2-wm/? And so on? * 2)* This brings me to another head-scratcher for me: wm.mgz. Should all subcortical structures fall within the main surface (including ventral DC)? Sometimes the main surface cuts into the hippocampus/amygdala, so do I have to add/delete voxels so it goes around it? I would think the pial and main surfaces should exclude these two structures. The pial and main surfaces are ~identical around the midline and subcortical structures; is this the desired result? If i want to change the main surface in general, what is the significance of the white voxels vs. grey voxels? I think I understand that the white voxels are there just so the surface will go around it. So, in theory, if I wanted the main surface to include all of the hippocampus, I could fill in white voxels for the hippocampus, and then run recon-all? If I delete grey voxels, will this change the main surface (I suppose this would be like the opposite of control points)? I read in some places that the WM volume produced by mris_anatomical_stats is taken from all the voxels that are "on" in wm.mgz. If this is the case, then the ventricles are included? Some parts of the dura are "on" in wm.mgz (although do not fall within ?h.white); would I have to go slice-by-slice deleting these annoying voxels? * 3)* Is the data from mri_segstats and mri_anatomical_stats reliable? I've seen threads saying mris_wm_volume and mris_volume are better, since the GM and WM data are calculated using the surfaces. I don't have the former (I'm using FS v3.0.4). I noticed the WM volume given by /mris_volume rh.white - /{sum of volumes of subcortical structures} is very close to that given by mri_segstats, which is similar to using mris_wm_volume. Is this correct? So, in the future, when I do recon-all for a subject, is it best to do it step-by-step, and make the edits as I go along? Thanks for the help, Chris

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pial misclassified
by abel cruz vadell 13 Dec '07

13 Dec '07

Hi everyone Checking the automatic pial segmentation of my MRI images in Freesurfer, I found some pixels misclassified as pial surface and I'm afraid of wrong cortical thickness measures in those regions. Is there any automatic tool to correct it? I attached two images with arrows signalizing the problem. Thanks for your help ______________________________________________ ¿Chef por primera vez? Sé un mejor Cocinillas. http://es.answers.yahoo.com/info/welcome

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mris_smooth and 'NoRandomness'
by Michael Harms 12 Dec '07

12 Dec '07

Hello, Is the 'NoRandomness' flag (and -seed flag) no longer relevant for 'mris_smooth'? That is, if I repeat mris_smooth using the same input, I always get the same output smoothed surface, which was not my expectation. Similarly, even if I explicitly chose different -seed values, the output is identical. thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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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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Freesurfer December 2007