Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

FDR versus mri_glmfit-sim with --cache option
by Antonella Kis 18 Jul '12

18 Jul '12

Dear FS team, I am doing a cortical thickness study using QDEC. I used FDR and got the following clusters: Generating cluster stats using min threshold of 3.8... Found 2 clusters Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4 superiorfrontal ============================================================ I need to get the cortical thickness values from each subject within this clusters so I am trying to use mri_glmfit-sim with --cache option and I wonder what value should I choose in this case for cache (2, 3.3 or 4) and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's results. I tried: mri_glmfit-sim \ --glmdir lh.L_frontal.glmdir \ --cache 3 neg \ --cwpvalthresh .05 \ --overwrite # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 0.02410 0.02820 949 precentral 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 0.00000 0.00040 1053 superiorfrontal so as you can see the clusters are the same but their Size and NVtxs is so different. What is wrong? Thank you for your time and help. Antonella

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sum of WM and GM coming out to be bigger than ICV after recon-all
by Ayaz, Muhammad 18 Jul '12

18 Jul '12

Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Labels for comparison
by John Drozd 18 Jul '12

18 Jul '12

Hello, I have successfully developed an automated algorithm combining pixel intensity-based and shape based approaches to segment the lateral ventricles. I have applied my algorithm to a small data set of 1.5 T1 ADNI images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI (subjects with Mild Cognitive Impairment) and 24 NEC (elderly controls). In my cases, particularly AD cases, I noticed that the segmentation of the lateral ventricles is connected to the third ventricle with foramina (usually 1 on a side or on both sides). Also, sometimes I find a connection with the posterior horn and third ventricle. I have researched CSF flow and from the literature, and all of these are real connections. I am near completion of developing an automated cropping scheme with a colleague to crop the third ventricle at these junctions. Our implementation is a combination of C++ code that we have developed and modified ITK classes. We have been viewing our segmented label maps in Slicer3 and generated 3D renderings using Slicer3's Model Maker module which is based on Marching Cubes. I have viewed a Freesurfer segmentation in Slicer3 based on a tutorial on the Slicer web site. I presented a poster of our results at the AIC and AAIC conference which I am at now in Vancouver, and a few people have asked me to compare my volumes with other methods. They were particularly interested in comparing my volumes with Freesurfer ventricle volumes and cross-sectional and longitudinal data. I was told and found csv files on the ADNI web site of Freesurfer analysis. I plan to correlate my values with Freesurfer's values, but I would be interested if Freesurfer also finds these connections between the third ventricle and lateral ventricles and also if it includes isolated temporal horn pieces when the horns are discontinuous due to the MRI not being able to resolve a very thin portion of the temporal horn. So, would it be possible, if I gave you a list of my ADNI subjects, for you to provide me the freesurfer label maps that correspond to the volumes in the csv files that are on the ADNI web site please? I could run Freesurfer but I would prefer having the label maps that exactly correspond to the Freesurfer ventricle volumes that are on the ADNI website. These would be from the two versions of Freesurfer noted on the ADNI web site in the ADNI Study Data/MRI image analysis link. Thank you, John Sent from my iPhone 4S

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Flip brain
by Tadeu Kubo 18 Jul '12

18 Jul '12

Hi Dear FS experts, Doug sent these links, but I can't download them. Do you have the new links? Download these filesftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregf… Thank you. Regards, Tadeu

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Hc segmentation: crosssectional stream with v4.5, longitudinal with v5.1
by Wenger, Elisabeth 17 Jul '12

17 Jul '12

Dear FreeSurfer experts, we have processed a dataset crossectionally within version 4.5, and then ran the longitudinal stream with v5.1. we are interested in the hippocampus segmentations and now i'm wondering whether i should go back and run the whole analysis from scratch with the newest version. I understand that it might or even will give me slightly different results, but would it also be the assumption that the new results would be somewhat more correct, that is anatomically more accurate, because maybe for example the processing has been optimized for hippocampal segmentation or anything like that in the newer version? Or would they just be different, as they would also be different when running it on a different computer, Mac or PC, OSX version, etc? Thank you very much for your help in advance!! Best wishes, Elisabeth

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I had a Computer Failure, how can I resume recon-all for base (longitudinal processing)
by Natacha Beck, Ms 17 Jul '12

17 Jul '12

Hello, I know that we can resume a recon-all command, if it's a cross-sectionnally process. In this case the command is: recon-all -make all -s subject But I had a power failure during a longitudinal study, when I try to execute : recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2' That's why I would like to resume this command, that's why I tried : recon-all -make all -sd . -s 'Test_base_22' But I received this error : ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \' So I tried this command: recon-all -make all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2' But I received the same error: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Subject 'Test_base_22': make all recon-all -s /Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22 -talairach -tal-check ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \' make: *** [/Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22/mri/transforms/talairach.auto.xfm] Error 1 Somebody can help me and tell me which command I need to execute. Natacha

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Memory allocation problem trac-all -prior
by Rui Lavrador 17 Jul '12

17 Jul '12

---------- Forwarded message ---------- From: Rui Lavrador <ruilavrador(a)gmail.com> Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Rui - How many voxels are in your diffusion volume? How many of them > are inside the mask? > > a.y > > > On Thu, 12 Jul 2012, Rui Lavrador wrote: > > Hi all, >> I'm running tracula and when doing the step: >> trac-all -prior -c single_subject >> >> After some time it gives this error: >> >> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice >> >> Cannot allocate memory >> >> I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is >> DTI with 64 directions. >> >> This happens many times? I need more memory? >> >> Best regards, >> >> -- >> Rui Lavrador >> >> >> >> > > 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<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. > > -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador(a)fmed.uc.pt e-mail2: ruilavrador(a)gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador(a)fmed.uc.pt e-mail2: ruilavrador(a)gmail.com

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Question on longitudinal statistics
by Kairys, Anson 17 Jul '12

17 Jul '12

Hi, In the longitudinal tutorial it states that: "In order to analyze your longitudinal data, you have different options. You could, e.g., open the stats text files in each tpN.long.templateID/stats/ dir, containing statistics such as volume of subcortical structures or thickness averages for cortical regions. These statistics can be fed (after conversion) into statistical packages to run whatever analysis you are interested in, such as linear mixed effects models (often used in longitudinal analysis). I am wondering what conversion this refers to? I would like to run the stats in SPSS without having to use qdec for now. Any help would be great Best Anson K. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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hippocampus subfilelds mask
by lorenzo pasquini 17 Jul '12

17 Jul '12

Dear Freesurfer experts, I successfully run a hippocampal subfield segmentation on anatomical data of one subject (resolution 1 mm^3). Now I am building hippocampal subfields masks. I used the FreeView interface to load the mgz volume files of hippocampal subfields. I saved each subfield separately, binarized and transformed it in my dimension space through marsbar (spm8). I tried as well the mri_binarize command with the codes for hippocampal subfields, but the extracted masks were strangely empty (no voxels found). Is this a right way and the simplest way to build hippocampal subfields ROIs? Is there any apparent error in these procedure? Binarized mask might overlap, is there any suggested threshold? Thank you very much, greets, Lorenzo Pasquini

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Re: [Freesurfer] white-gray contrast algorithm
by Fred Lado 17 Jul '12

17 Jul '12

I found a thread (with same subject line) in the archive that referred to Freesurfer tools to measure white-gray contrast, but I could not find anything further on where the information resides. Is there a way to measure white-gray contrast in the manner described in several papers (difference in signal intensity 1/2 mm above and below white-gray junction)? I am interested in using these measurements to identify cortical dysplasias in patients with epilespy. Thanks, -- Fred Lado, MD PhD Chief of Service, Neurology - Moses and North Divisions Director, EEG Laboratory Montefiore Medical Center Associate Professor of Clinical Neurology 718-920-8499 (office) 718-920-9830 (appointments) 718-324-3730 (fax) ladofred(a)gmail.com

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Freesurfer July 2012