Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

voxel size issue
by Hibert, Matthew Louis 25 Mar '16

25 Mar '16

Hi Freesurfer developers, Some structural images I'm working with only display properly in the axial plane, in which they were acquired; the sagittal and coronal views are distorted and appear stretched out in the superior-inferior direction, screenshots of this are attached. Freesurfer (both freeview and mri_info/mri_convert) incorrectly read the superior-inferior voxel dimension as 19mm when it is in fact 0.5mm. Reading the header with matlab shows that the header correctly specifies "slice thickness" as 0.5mm. There is another field, gap between slices, which has a value of 19mm, and freesurfer appears to be reading this field instead of the slice thickness field. This problem exists in both version 5.3 and the current dev version. The images display correctly in all 3 planes on both the MRI console computers and in Osirix. Is there a way to have Freesurfer read the slice thickness field instead so the images will display properly? I can point you to some data with this issue if that would be helpful. Thanks, Matt

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Gray-white segmentation
by Dr. Benson 25 Mar '16

25 Mar '16

I'm new to FreeSurfer. Trying to do volumetric analysis on MPRAGE data but on half of the studies the results are poor. Specifically, the gray matter volume is very small due to a poor segmentation of the white matter which includes much of the cortical gray matter. The contrast to noise is good and not sure why I got a good result on some and not others. Could use some help on this, please. Randy Benson, M.D. -- Medical Director--Center for Neurologic Studies *43000 W. 9 Mile Road * *Novi, MI 48375* *CNS Phone (248)277-3334* *Cell: (248) 227-9814* *Fax (586) 566-0178* Web: www.NeurologicStudies.com <http://www.neurologicstudies.com/> -- ***NOTICE*** The documents accompanying this email transmission contain confidential information belonging to the sender, which is legally privileged. The information is intended only for the use of the individual(s) or entity(ies) named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or the taking of any action in reliance on the contents of this emailed information is strictly prohibited. If you have received this email in error, please immediately notify us by telephone at 248-277-3334 to arrange for return of the original documents to us. Thank you.

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FSFAST mkcontrast-sess with spmhrf 2 question
by Joseph Dien 25 Mar '16

25 Mar '16

Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

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Cortical thickness average
by Sahil Bajaj 25 Mar '16

25 Mar '16

Hello FreeSurfer community, I calculated cortical thickness for 100 controls following the instructions described here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was wondering if there is any way to average the thickness over these 100 lh.thickness.fsaverage.mgh files to get one final lh.thickness.fsaverage.mgh I am interested in calculating cortical thickness for 15 previously defined ROIs, but I do not want to calculate 15x100 text files using mri_segstats i.e. 15 text files for each subject and then average over those but I would rather prefer to average over 100 lh.thickness.fsaverage.mgh files first and then calculate thickness for each ROI to get 11 text files. Any help would be really appreciated. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?
by Elijah Mak 25 Mar '16

25 Mar '16

Hi Kirstie, Yes indeed there were 3 subjects at the bottom-left of the plot. To account for PV, I eroded the boundaries using *-seg-erode 1* during the *mri_segstats* stage, and this resulted in a few subjects with no data for the WM entorhinal region (although these were saved as "0" in the .stats file). Do people generally do this for DTI studies? All good now. Many thanks again, Kirstie. Best Wishes, Elijah

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FA and MD *positively* correlated within same regions ?
by Elijah Mak 24 Mar '16

24 Mar '16

Hi Freesurfer Community, I recently used mri_segstats to extract FA and MD as suggested here: http://freesurfer.net/fswiki/FsTutorial/Diffusion Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at some of the correlations between FA and MD in the same regions, and came across a few interesting ones. wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001 ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020 wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001 As I understand, a clear-cut interpretation especially with regards to FA changes is not so easy! But could someone discuss / speculate as to why FA and MD could be positively correlated within the entorhinal WM region? That was found separately within a group of a elderly healthy controls and a group of dementia subjects. Thank you for your time! Best Wishes, Elijah

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Re: [Freesurfer] Trac-all -path Segmentation error
by Anastasia Yendiki 24 Mar '16

24 Mar '16

Hi Katherine - The dlabel/ directory is created during the -prep step, when the structural segmentation gets mapped from T1 to diffusion space. However bedpost may still run fine without the dlabel/ directory. It seems that the problem is fairly early in the -prep step. Any errors there? Best, a.y On Wed, 23 Mar 2016, Katherine Damme wrote: > Hey Anastasia, > > > Although the bedpost appears to complete properly the dlabel/diff is not > being created during the bedp step. I am not sure how or why this error is > occurring. That would, it appears, definitely be the cause of the failure. > However, I am not getting an error during the prep or the bedpost stage, and > so I am still completely lost any advice would be deeply appreciated! > > Thank you, > > KD > > On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Katherine - Do the freesurfer segmentations look ok? What > about the registration from structural to diffusion? You can > inspect those quickly with: > > freeview dmri/dtifit_FA.nii.gz > dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3 > > Hope this helps, > a.y > > On Sun, 3 Jan 2016, Katherine Damme wrote: > > First I should note that using the same scripts I > completed 52 participants successfully and am > currently trying to > batch process the newest 42 participants that are > only failing at the path level. Upon Visual > Inspection they all > appear normal (with the exception of the one > attached). After carefully comparing a random sample > of 5 from each > group images from the files that failed versus the > files that were successful, I found: > > 1. The range of values in the mean_ph1samples in the > successful ( i.e. -3.00 to 87.30 ) differed from the > failures > (i.e. -2 to 17) (the successful samples varied on > their high end from 50-114 but the failures were on > the 5-24 > range) > 2. The range of values in the mean_th1samples in the > successful ( -0.02 to 19.12) differed from the > failures > (-0.00267 to 7.176) (the successful samples varied > on their high end from 19-17 but the failures were > on the 3-10 > range) > 3. Some, but not all (2/5), mean_S0samples, had a > abnormal range in successful (0 to 19998.4) compared > to the > unsuccessful (0 to 709.96) > > However, I understand that the diffusion units are > likely arbitrary and not sure these patterns will > hold in a > larger sample. > > I know this is a lot of confusing information and so > in response to your question. After an initial > inspection > there are two types of output: > 1. data that appears visually normal with a slightly > altered range. > Should I be concerned about the range if all other > data looks fine? > > 2. data that appears visually normal with a normal > range and bizarre merged files. > What do you think could be a cause of these odd > merged files? > > > > > On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Katherine - Have you looked at any of the > intermediate images? Do they look normal? > > a.y > > On Mon, 21 Dec 2015, Katherine Damme wrote: > > Hello Everyone! > > It looks as though my prep and bedp > stages completed properly, but the prep stage ends > in a > segmentation > errror. > > See attached and let me know your > thoughts. I would prefer not to have to redo all > steps if > possible! > Thank you! > > > > > 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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Re: [Freesurfer] Cortical thickness average
by Elijah Mak 24 Mar '16

24 Mar '16

Hi Sahil, I did something similar recently. I believe you can use mri_concat with the -mean option to create an average map of the group. Another option might be make_average_subject? https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject Best Wishes, Elijah

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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?
by Elijah Mak 24 Mar '16

24 Mar '16

Hi Alshikho <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> , Yes, I am sure :) Same sequence for everyone. Just to add. FA and MD were significantly negatively correlated for the other regions including the fusiform, precuneus, hippocampus, thalamus, etc. So I am very curious about what could be going on with the ERC here? Best Wishes, Elijah

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ROI within subject
by Ji Won Bang 24 Mar '16

24 Mar '16

Dear. Freesurfer experts. Hi. How are you? I have a question about making ROI. This might be a naive question, but any input would be greatly appreciated. I preprocessed scans per run, thus I have register.dof6.dat file inside all run epi directories. Then, I made ROIs per single subject based on the single subject's functional contrast map using the command: tksurfer replay06 lh inflated -curv -gray I overlayed the single subject's contrast result sig.nii.gz (obtained from 3 runs) and the registration file in 1 run(register.dof6.dat in 1 among 3 runs), then I cut the plane and then flattenr the cortex, made ROI. While trying to check the ROIs, I realized that this ROI seems to be slightly different depending on which register.dof6.dat I use (I tried all 3 runs' register.dof6.dat when overlaying). tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01 I thought ideally, this functional ROI should be the same across all runs if thes register files are perfectly registering each functional sans to anatomical scan. Is this a usual way when people make ROI based on functional contrast map per each subject? The way I did in the past did not have this kind of problem because I did motion correction as targetting the first EPI (aligning all images to the first EPI) and then used only 1 (same) register.dat file.. Please share your idea with me. Thank you very much. Best, Ji Won

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