Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

20% changes
by Jessica Liu 28 Jul '11

28 Jul '11

Hi, We found 20% differences in temporal lobe brain volume and ca. 5% difference in the hippocampus volume between two data sets of a young normal volunteer scanned 2 days apart. We use the one-step 19 hours recon-all -all procedure and directly sum select values taken from the lh.aparc.stats, rh.aparc.stats, and wmparc.stats. The values summed were based on information given from https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-April/005000.html My question is, are these observations normal for Freesurfer? Any comments are greatly appreciated. Thanks! -- Pom & Jessica

3 8

Corrections for the Pial surface
by Antonella Kis 28 Jul '11

28 Jul '11

Hi Bruce, Thank again for your advice. I am not sure about the data collection but I will find out soon. In the mean time I have two more questions: 1). The FS tutorial shows for the surface outlines (by loading the -surfs) three line: the yellow indicating the white surface, the red for the pial and a green line for the orig data. When I plot the surfs I have only the yellow and red line. Can I get the green line somehow? 2). I suppose the two important brain structures, amygdala and hippocampus must be included in the pial surface as a grey matter (I hope I am right) . If they are not enclosed in the pial surface is there a way to resolve this issue? How I should edit the pial surface in this case? How important is to have them enclosed for my cortical thickness studies and for the GLM group analysi? Thank you very much. Antonella

3 6

Correction for head size - Total hippocampal volume and subfield volume
by New Fei Ho 28 Jul '11

28 Jul '11

Hi, I have two questions regarding ICV correction for total hippocampal volume (from aseg.stats) and for hippocampal subfield volumes. 1) Total hippocampal volume: I am using the mri_label_volume script that uses the atlas normalization factor as an estimate for total ICV two T1-weighted scans (T1 = 1100ms, TE = 3.39ms, TR = 2530 ms, FOV = 256) and a third T1-weighted (T1 = 1100ms, TE = 1.54ms, TR = 2200ms, FOV = 192) conducted in the same session. The pearson's correlation coefficient between the left hippocampal volume of the 3 scans and their corrected volumes (35 healthy subjects) are .998, .662 and .997.For the right hippocampal volumes, the coefficients are .678, .995 and .893. If the eTIV accounts for variances in head, are the r-values too high (especially .998, .995)? 2) As for hippocampal subfield volume correction for head size, can I similarly apply the same method, or would you recommend just using total ICV (from aseg.stats) as a covariate? Thanks, New Fei

1 0

mri_surfcluster for cortical volume comparisons
by Yolanda Vives 28 Jul '11

28 Jul '11

Dear freesurfers, I would like to obtain the cluster size (in mm3) and coordinates of the maxima of a cortical volume comparison using mri_surfcluster. mri_surfcluster --in $PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh --hemi rh --subject fsaverage --thmin 2 --thmax 7 --sign pos --surf pial --no-adjust --o ./concro --ocn ./cluster_number --olab ./grouplabel_concro --sd $SUBJ_DIR --sum ./concro_sum Would it be correct. Regarding the results that I obtain, I have some questions: - Which surface do I have to load? pial, orig? - In the summary file, the cluster size is given in mm2, is it possible to obtain it in mm3 (I am analysing cortical volume)? Thank you for your help, Yolanda

3 5

extracting mean cortical thickness
by Knut J Bjuland 28 Jul '11

28 Jul '11

Hi. I am trying to extract the mean cortical thickness in a group, and the mean cortical thickness when dividing the group by gender. There was an faq about cortical thickness but it gave none answer. I have tried to use aparcstats2table, and I notice that this was done in this paper https://surfer.nmr.mgh.harvard.edu/ftp/articles/salat04-thinning.pdf. How can I instruct Qdec to export thickness data or another tool in Freesurfer? Best regards Knut J

1 1

Voxel Displacement When Loading DICOM Images
by Sullivan, Patrick M. 27 Jul '11

27 Jul '11

Hi All, I'm a new Freesurfer user, and I'm trying my best to pick it up on my own with the wealth of documentation available. Unfortunately, I can't seem to find any mention of this particular problem in the wiki or in the archives of this newsletter, so I hope someone can help. Please forgive me, I'm still learning, and I may not know the correct terminology for some items; I will try to describe the problem as best I can. I'm attempting to simply view a set of DICOM images (T1 format) with TkMedit before I convert and/or process them at all, just to make sure they are loading properly. The 120 slices load fine using the Philips proprietary DICOM viewer, but for some reason when I load the image in TkMedit, a strange series of displacements occur. In each plane at least 1 or 2 "lines" appear, dividing the brain so that the entire image has been shifted (by perhaps a voxel or half a voxel) beyond this line. This shift can happen in any direction (anterior/posterior, lateral/medial, superior/inferior). For instance, when viewing the image in the sagittal plane, one of these lines appears at approximately the pre-central gyrus, traveling straight "up and down" so that everything in front of the line is shifted as though I had scrolled 1 additional slice sagitally through the brain. (In the lateral/medial direction, the temporary "z" axis when viewing the image sagitally, not the true superior/inferior z axis). This was immediately visually obvious because some slices of the brain have starkly different contrast, so when different parts of the brain were being shown at different slices, it really popped out. However, other similar lines are simply shifted "up/down" or "forward/back" one voxel, making them less obvious but still problematic. All of these lines are constant, in the same location for each slice. I am really not sure what is causing this, although my first tentative guess is to wonder whether the images were perhaps acquired at an oblique angle and TkMedit is trying to compensate for that in some way. Beyond that though, I really do not have any guesses. Does anyone have any ideas about what might be going on, and how I might fix it? I apologize if I have stated any of this poorly. Any help or pointers in the right direction would be appreciated tremendously. Thank You, -Patrick

3 2

WM and ASEG edition... recon-all continue command...
by Gonzalo Rojas Costa 27 Jul '11

27 Jul '11

Hi I editted the wm.mgz and aseg.mgz files... Which recon-all command must I use to continue the processing ?... Sincerely, Gonzalo Rojas Costa

2 5

Loading atlases
by Antonella Kis 26 Jul '11

26 Jul '11

Hi, I would like to check if my subcortical segmentation is correct so I was running: tkmedit SUBJECT1 brainmask.mgz \ -aux T1.mgz -surfs \ -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt 1). Pial (red line), and white (yellow line) surfaces are shown and I wonder how I can add a green lie for my orig surface? 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the original/correct atlas so I can see if my segmentation is correct? Thank you very much. Antonella

2 1

Reproducible Qdec error color bar not updated when clicking reverse value.
by Knut J Bjuland 26 Jul '11

26 Jul '11

Hi When I click on reverse values in Qdec the color on the hemisphere will change, but the color bar at the bottom on the screen will stay the same. Is there anything I can do to force Qdec to change the color bar at the bottom of the screen? I am send along to attachment one with reverse values and one without reversing the values. To reproduce this error I have sent a picture of the same correlation with one exception I have clicked on reverse value on the file named error.jpg. Best regards Knut J

3 2

Unknown label
by Antonella Kis 26 Jul '11

26 Jul '11

Hi Bruce, I forgot to ask why my data does not include an unknown region in my aparc.stats file? My stats data starts with bankssts region and continue with caudalanteriorcingulate, etc. Do I need to have the unknown region if I use the new version of the FS 5.1.0? Thank you. Antonella

1 0

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Freesurfer July 2011