Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Re: [Freesurfer] optseq2 parameters setup
by Greve, Douglas N.,Ph.D. 16 Jul '19

16 Jul '19

You are probably interested in the power (ie, "can I detect an effect with this many trials scheduled in this way?"). It is not possible to answer this question without an effect size. Having said that, I generally feel comfortable when the VRF is 20-40. Note that this assumes an FIR (not assuming a shape to the hemodynamic response) and dPSD=TR. If you assume a shape, you will get much more power out of it (assuming your assumed shape is close to correct:). On 7/16/19 9:51 AM, Tugce Duran wrote: > > External Email - Use Caution > > Thank you, Dr. Greve! This was helpful. > > When we look at the .sum file, what are the reference ranges for Eff > and VRF avg? > > I saw 20-40 for VRF on the help page but wasn’t fully sure. > > Thanks! > > Tugce > > *Tugce Duran* > *Graduate Student, Biomedical Sciences MS Program/ > /Neuroscience Concentration | **Section on Gerontology & Geriatric > Medicine, WFSM* > 2color > *Graduate Programs in Biomedical Sciences* > 525 Vine Street, Suite 150, Winston-Salem, NC 27101** > > *(*317-893-9100 *| ****_tduran(a)wakehealth.edu > <mailto:tduran@wakehealth.edu>_| |Image result for linked > inlinkedin.com/in/tugceduran/ <http://linkedin.com/in/janesmith/> > The information contained in this message is privileged and > confidential information intended for the sole use of the addressee. > If the reader of this message is not the intended recipient, or the > employee or agent responsible for delivering it to the intended > recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. > If you have received this message in error, please notify the person > listed above immediately by e-mail, and delete the original message > and attachments. > > *From:*Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > *Sent:* Monday, July 15, 2019 11:03 PM > *To:* Tugce Duran <tduran(a)wakehealth.edu>; Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: optseq2 parameters setup > > On 7/15/2019 12:50 PM, Tugce Duran wrote: > > * External Email - Use Caution * > > Hi Dr. Greve, > > I am interested in designing the Face Name Associative Memory Exam > (FNAME) fMRI task for our study. > > There are *80* face-name pairs that we will use and the duration > can be between 3.5 and 4.75 secs. I have used the following command: > > *optseq2 --ntp 200 --tr 2 --psdwin 0 32 2 --ev facename 4 80 > --nkeep 3 --o trial2 --tnullmin 0 --tnullmax 6 --nsearch 10000* > > Total scan time appx 6-7 mins. > > Q1: For NULL, why do we have only 2 sec and 4 sec jitters? Can we > change the variety amount of the jitters? Are more jitters good or > bad (instead of just having 2 secs and 4 secs, let’s say we get > 0.25, 1, 2, 3 and 4 secs) ? > > It always makes the NULL durations a integer multiple of the dPSD. You > set this to 2 (--psdwin 0 32 2). If you are assuming the shape to the > hemodyamic response (eg, the canonical SPM HRF), then it won't matter > much if you decrease it to 1 or less). The benefit of jitter in that > case depends more on the psychology than the signal processing. > > Q2: For the event design I am interested in above, what would be > the “best” parameters used? > > Usually, you set the total time for the NULL to be equal to that of a > stimulus type. In this case, you have one stimulus type presented for > a total of 320 sec (4*80), so you could set the scan duration to be > 320*2=640sec=10min 40sec. That would be optimum for testing your > stimulus against baseline, but that is probably not what you are > planning to do. > > *Trial2-001.par:* > > *0.0000 1 4.000 1.0000 facename* > > * 4.0000 1 4.000 1.0000 facename* > > * 8.0000 1 4.000 1.0000 facename* > > *12.0000 0 2.000 1.0000 NULL* > > *14.0000 1 4.000 1.0000 facename* > > *18.0000 1 4.000 1.0000 facename* > > *22.0000 1 4.000 1.0000 facename* > > *26.0000 1 4.000 1.0000 facename* > > *30.0000 1 4.000 1.0000 facename* > > *34.0000 1 4.000 1.0000 facename* > > *38.0000 1 4.000 1.0000 facename* > > *42.0000 0 4.000 1.0000 NULL* > > *46.0000 1 4.000 1.0000 facename* > > *50.0000 1 4.000 1.0000 facename* > > *54.0000 1 4.000 1.0000 facename* > > *58.0000 1 4.000 1.0000 facename* > > *62.0000 1 4.000 1.0000 facename* > > *66.0000 1 4.000 1.0000 facename* > > *70.0000 1 4.000 1.0000 facename* > > *74.0000 0 2.000 1.0000 NULL* > > *76.0000 1 4.000 1.0000 facename* > > *80.0000 0 2.000 1.0000 NULL* > > *82.0000 1 4.000 1.0000 facename* > > *.* > > *.* > > *.* > > *.* > > ** > > *372.0000 0 4.000 1.0000 NULL* > > *376.0000 1 4.000 1.0000 facename* > > *380.0000 1 4.000 1.0000 facename* > > *384.0000 1 4.000 1.0000 facename* > > *388.0000 1 4.000 1.0000 facename* > > *392.0000 1 4.000 1.0000 facename* > > *396.0000 1 4.000 1.0000 facename* > > Thank you in advance! > > Tugce > > *Tugce Duran* > *Graduate Student, Biomedical Sciences MS Program/ > /Neuroscience Concentration | Section on Gerontology & Geriatric > Medicine, WFSM* > 2color > *Graduate Programs in Biomedical Sciences* > 525 Vine Street, Suite 150, Winston-Salem, NC 27101 > > *(*317-893-9100 *| ****_tduran(a)wakehealth.edu > <mailto:tduran@wakehealth.edu>_| |Image result for linked > inlinkedin.com/in/tugceduran/ [linkedin.com] > <https://urldefense.proofpoint.com/v2/url?u=http-3A__linkedin.com_in_janesmi…> > The information contained in this message is privileged and > confidential information intended for the sole use of the > addressee. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivering it > to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is > strictly prohibited. If you have received this message in error, > please notify the person listed above immediately by e-mail, and > delete the original message and attachments. >

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Problem while fix topology
by Li Ma 16 Jul '19

16 Jul '19

External Email - Use Caution Hi Everyone! I have met a problem that when I run the recon-all command, freesurfer always stuck at fix topology and dont give any files modify or terminal return for days. Could you please to help me solve this problem? Thanks!

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question for files recon-all generated
by ping cao 16 Jul '19

16 Jul '19

External Email - Use Caution Dear expert, I want to know if the *norm.mgz* is already linearly registered？ And is the *T1.mgz *not linearly registered? They are all generated from *recon-all. * Is there any file non-linearly registered? Best wishes, ping

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Question about coordinates in Freesurfer
by Zhi Li 16 Jul '19

16 Jul '19

External Email - Use Caution Dear Freesurfer experts, Now I have an annotation file in fsaverage space and a MNI voxel coordinate of one subject. May I ask how could I know if this coordinate is in one parcel of the annotation file? There are many coordinates that I cannot check it one by one in Freeview. In addition, if this is a native image coordinate how could I check whether it is in a parcel then? An additional question is whether the spaces of all the files in folder "mri" generated by recon-all are native individual space? What do the files 'orig.mgz', norm.mgz'', 'brainmask.mgz', 'brain.mgz' and 'T1.mgz' refer to? They are very similar to each other, with skull-stripped or not. Is there any document on it I could reference? Looking forward to your kind suggestions, Many thanks and best regards, Lizhi

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freeview
by Juan Rivas 16 Jul '19

16 Jul '19

External Email - Use Caution I try again with fortran, uploaded it again, and now I get this message: jcrn12@jcrn12-VirtualBox:~$ freeview This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) Best regards, JC.

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Viewing Uncorrected Significance Map in Freeview
by Marie Hill 15 Jul '19

15 Jul '19

External Email - Use Caution Hi everyone, I have just finished running glmfit. When I try to load the significance maps in freeview, they appear to load for a moment and then disappear, just showing the brain volume without any highlighted areas of significance. Does anyone have any idea why this could be? I ran the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5 -viewport 3d Kindest Regards, Marie

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How to Divide the Surface Parcellations of the Brain
by Mahshid Fouladivanda 15 Jul '19

15 Jul '19

External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation file? I mean what information, it needs? Regards Mahshid

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make_average_subject error: could not load norm volume from (null)
by Mads Jensen 15 Jul '19

15 Jul '19

External Email - Use Caution HI FreeSurfer Developers, I'm attempting to create an average subject make_average_subject but I get the error message the following error when I run the make_average_command: Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I cannot find anything similar on the mailing list. I hope anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.4 LTS 3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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A Question Regarding Topology Correction
by Maedeh Khalilian 15 Jul '19

15 Jul '19

External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh

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Re: [Freesurfer] optseq2 parameters setup
by Greve, Douglas N.,Ph.D. 15 Jul '19

15 Jul '19

On 7/15/2019 12:50 PM, Tugce Duran wrote: External Email - Use Caution Hi Dr. Greve, I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI task for our study. There are 80 face-name pairs that we will use and the duration can be between 3.5 and 4.75 secs. I have used the following command: optseq2 --ntp 200 --tr 2 --psdwin 0 32 2 --ev facename 4 80 --nkeep 3 --o trial2 --tnullmin 0 --tnullmax 6 --nsearch 10000 Total scan time appx 6-7 mins. Q1: For NULL, why do we have only 2 sec and 4 sec jitters? Can we change the variety amount of the jitters? Are more jitters good or bad (instead of just having 2 secs and 4 secs, let’s say we get 0.25, 1, 2, 3 and 4 secs) ? It always makes the NULL durations a integer multiple of the dPSD. You set this to 2 (--psdwin 0 32 2). If you are assuming the shape to the hemodyamic response (eg, the canonical SPM HRF), then it won't matter much if you decrease it to 1 or less). The benefit of jitter in that case depends more on the psychology than the signal processing. Q2: For the event design I am interested in above, what would be the “best” parameters used? Usually, you set the total time for the NULL to be equal to that of a stimulus type. In this case, you have one stimulus type presented for a total of 320 sec (4*80), so you could set the scan duration to be 320*2=640sec=10min 40sec. That would be optimum for testing your stimulus against baseline, but that is probably not what you are planning to do. Trial2-001.par: 0.0000 1 4.000 1.0000 facename 4.0000 1 4.000 1.0000 facename 8.0000 1 4.000 1.0000 facename 12.0000 0 2.000 1.0000 NULL 14.0000 1 4.000 1.0000 facename 18.0000 1 4.000 1.0000 facename 22.0000 1 4.000 1.0000 facename 26.0000 1 4.000 1.0000 facename 30.0000 1 4.000 1.0000 facename 34.0000 1 4.000 1.0000 facename 38.0000 1 4.000 1.0000 facename 42.0000 0 4.000 1.0000 NULL 46.0000 1 4.000 1.0000 facename 50.0000 1 4.000 1.0000 facename 54.0000 1 4.000 1.0000 facename 58.0000 1 4.000 1.0000 facename 62.0000 1 4.000 1.0000 facename 66.0000 1 4.000 1.0000 facename 70.0000 1 4.000 1.0000 facename 74.0000 0 2.000 1.0000 NULL 76.0000 1 4.000 1.0000 facename 80.0000 0 2.000 1.0000 NULL 82.0000 1 4.000 1.0000 facename . . . . 372.0000 0 4.000 1.0000 NULL 376.0000 1 4.000 1.0000 facename 380.0000 1 4.000 1.0000 facename 384.0000 1 4.000 1.0000 facename 388.0000 1 4.000 1.0000 facename 392.0000 1 4.000 1.0000 facename 396.0000 1 4.000 1.0000 facename Thank you in advance! Tugce Tugce Duran Graduate Student, Biomedical Sciences MS Program Neuroscience Concentration | Section on Gerontology & Geriatric Medicine, WFSM [2color] Graduate Programs in Biomedical Sciences 525 Vine Street, Suite 150, Winston-Salem, NC 27101 • 317-893-9100 | • tduran(a)wakehealth.edu<mailto:tduran@wakehealth.edu> | |[Image result for linked in]linkedin.com/in/tugceduran/<http://linkedin.com/in/janesmith/> The information contained in this message is privileged and confidential information intended for the sole use of the addressee. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, please notify the person listed above immediately by e-mail, and delete the original message and attachments.

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Freesurfer July 2019