Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

Changing Thresholds in dmri_pathstats: --pthr option not changing results
by Adam Schadler 11 Mar '19

11 Mar '19

External Email - Use Caution Dear freesurfer community, I have been trying to experiment a bit with the dmri_pathstats command that TRACULA uses to compute tract statistics. I read previously that one could change the default threshold value that stats are computed with by using the "--pthr .##" option. (I was curious about using this since I often run into the peculiar problem of some tracks, e.g. forceps major/minor, having mostly normal looking path.pd maps, with a few voxels having unusually high values, thus potentially biasing results. These tracks are often set at abnormally high thresholds when visualizing the tracks. e.g. a forceps major normally has a threshold [30,45], while some may be thresholded as high 100 or 150, making the tract look problematic). I experimented by running the dmri_pathstats command with a few different values for "--pthr .##": * --pthr .01 * --pthr .05 * --pthr .10 * --pthr .20 * --pthr .80 * --pthr 1.00 However, the outputted "pathstats.overall.txt" and "pathstats.byvoxel.txt" files are all identical. Suspecting a potential bug, I did a few more tests, with values such as: * --pthr 2.0 * --pthr 100 * --pthr 50000000000000 * --pthr hi * --pthr goodbye * --pthr Interestingly, all of the outputted "pathstats.overall.txt" and "pathstats.byvoxel.txt" files were all identical to the previous six tests. The program does not return an error message either. Is this a potential bug? Or was the "--pthr" functionality removed from dmri_pathstats? Incidentally, I am using freesurfer version 5.3.0. Maybe this was updated in a further release? Thank you for any clarification! Sincerely, Adam Schadler

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Welch's t-test for HOV violation
by Hannah CK 11 Mar '19

11 Mar '19

External Email - Use Caution We are conducting t-test comparisons across groups in which there is a large discrepancy in group sizes. HOV is violated. I've searched for ways to run Welch's t-test in FreeSurfer (or a similar analysis that does not assume homogeneity of variance) but am not finding one. Could anyone please advise on how to do this? Thank you.

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Recon-all, hippocampal segmentation issue
by Faezeh Vedaei 11 Mar '19

11 Mar '19

External Email - Use Caution Hello Freesurfer Developer I have an issue of running Freesurfer command on the Mac terminal in order to do recon-all and hippocampal segmentation. I used the command line as I provide here, but it shows me an error message due to can not find the input file (.nii)! This is so weird as the .nii input data is in the directory I am running this command. Really appreciate your help if you take a look at my command line, input data and error message and let me know how I can resolve this issue. 1-Freeaasurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2-Command: recon-all -all -i CID750.anat.nii -hippocampal-subfields-T1 ERROR: cannot find CID750.anat.nii 3- Platform: MacOS Mojave, Version 10.14.3 (18D109). Thanks Faeze

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mri_glmfit-sim cluster correction threshold inquiry
by Arsenije Subotic 08 Mar '19

08 Mar '19

External Email - Use Caution Hello, I am planning on running a correction for multiple comparisons, and I was hoping to use a vertex wise cluster forming threshold of 1.3, however after reading more when I ran the mri_glmfit-sim —help command it recommends using the permutation test if you are planning on using 1.3 as a threshold. Is there any reason why it is not recommended to use the 1.3 cluster threshold? My study is fairly exploratory so I was hoping to be a bit more lenient when it comes to adjusting the threshold. Thanks! Arsenije

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projfrac question
by Nasiriavanaki, Zahra 08 Mar '19

08 Mar '19

Dear Freesurfers Hi I was trying to look at the activation in different cortical layers in a single subject. I ran my preproc-sess command three times, once without using -projfrac flag, once -projfrac 0.5 and lastly -projfrac 0.2 The activation patterns are exactly the same. My voxel sizes are 1.1*1.1*1.1 . My question is: 1-Is it normal that the activations do not change at all the more I get closer to white matter? 2-when I use -projfrac 0.2 , does it mean that I am averaging the activation between white matter layer to 0.2 of gray matter layer? Or is it averaging the activation between pial surface to 0.2 gray matter? I hope my questions are clear. Thanks Mona

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Re: [Freesurfer] Accounting for family relation in FS
by Greve, Douglas N.,Ph.D. 08 Mar '19

08 Mar '19

Yea, the real hard part is figuring out how to model the twins that are split between groups. You might be able to create a bunch of groups. If you've already created a design in FSL that you like, you can extract the design matrix and use it in mri_glmfit with the --X option. Not sure about correcting for multiple comparisons though On 3/8/19 3:13 AM, Julian Macoveanu wrote: External Email - Use Caution Thank you for the reply. The original idea was to have an ANOVA with a group factor “diagnosis” with three levels. We could use an F-test to check for an effect of diagnosis and then perform 3 pairwise group tests (LR vs HR, LR vs ILL, HR vs ILL). Would it help to only implement the two-sample group tests? However, the critical issue to account for correlated data remains since about 80% of the subjects have their co-twin in the same group. The idea behind the model that has a variable with 1s for each twin pair is to model out each pair’s mean. I implemented the model I described in the FSL GLM and estimated with FEAT for the functional data of the group. The second option I had was to perform a permutation based estimation as implemented in PALM and restrict the permutations to between pairs and single subjects. Would any of these options work in FS? Maybe clustering the subjects somehow? Julian

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Re: [Freesurfer] Extraction of anatomical locations using Matlab
by Sparsh Jain 07 Mar '19

07 Mar '19

External Email - Use Caution Good evening. Thanks a lot for the help. It worked ! While most of the labels were correct, the matlab script returned the wrong location for one point . The script returned the label 'right cerebral white matter' for a point that seems to lie in the middle of the right amygdala. I have attached the screenshots. I do not think that there is a white matter area close enough to confuse the script. Could you tell me why this may have occurred? When I write the line "crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1" , is there an error due to rounding in the conversion? I was planning to inflate a sphere around each electrode point and get the neighboring anatomical regions as well. Sparsh

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arsenije Subotic 07 Mar '19

07 Mar '19

External Email - Use Caution Hi Doug, I realized this error a couple of days ago and now it works. Thank you, Arsenije

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Accounting for family relation in FS
by Julian Macoveanu 07 Mar '19

07 Mar '19

External Email - Use Caution Dear FS List, (apologies for reposting under different title) I wanted to check if my GLM design for a surface based analysis is sound. I am new to FS so please don’t skip over details. I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin pairs may be present in the same group (e.g both are in the low-risk) or between groups (one of them in high-risk one in affected). Not all twins have their co-twin in the analysis though. In order to account for with-pair variance correlation I was wondering if this FSGD example with 9 subjects might do it or if there might be better options. GroupDescriptorFile 1 Title … Class LR Class HR Class ILL Variables age sex TIV Pair_no1 Pair_no2 Pair_no3 Input subject1 LR 30 M 123456 1 0 0 Input subject2 LR 30 M 123456 1 0 0 Input subject3 LR 23 F 123456 0 0 0 Input subject4 HR 20 F 123456 0 1 0 Input subject5 HR 21 F 123456 0 0 1 Input subject6 HR 22 M 123456 0 0 0 Input subject7 ILL 20 F 123456 0 1 0 Input subject8 ILL 21 F 123456 0 0 1 Input subject9 ILL 35 F 123456 0 0 0 I do have 60+ pairs so it will be a lot of variables. I know that PALM has an options to provide an exchangeability file, but FsPalm seems to perform corrections for multiple comparisons only. Julian

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Gray matter segmentation
by Maxime Perron 07 Mar '19

07 Mar '19

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Freesurfer March 2019